diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 00000000..37b690f3 --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,41 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python package + +on: + push: + branches: [ "master" ] + pull_request: + branches: [ "master" ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11"] + + steps: + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest + if [ -f test-requirements.txt ]; then pip install -r requirements.txt -r test-requirements.txt; fi + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest + run: | + python -m pip install . + pytest tests/test_dr7sample.py diff --git a/.github/workflows/static.yml b/.github/workflows/static.yml new file mode 100644 index 00000000..93dd8948 --- /dev/null +++ b/.github/workflows/static.yml @@ -0,0 +1,43 @@ +# Simple workflow for deploying static content to GitHub Pages +name: Deploy static content to Pages + +on: + # Runs on pushes targeting the default branch + push: + branches: ["master"] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +permissions: + contents: read + pages: write + id-token: write + +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + # Single deploy job since we're just deploying + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Setup Pages + uses: actions/configure-pages@v5 + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + # Upload entire repository + path: './docs/_build' + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/README.md b/README.md index bf3d4127..85db4785 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,10 @@ ## PyQSOFit: A code to fit the spectrum of quasar +### Getting Started + __See the [example](https://nbviewer.org/github/legolason/PyQSOFit/blob/master/example/example.ipynb) demo notebook for a quick start tutorial__ -We provide a brief guide of the Python QSO fitting code (PyQSOFit) to measure spectral properties of SDSS quasars. The code was originally translated from Yue Shen's IDL code to Python. The package includes the main routine, Fe II templates, an input line-fitting parameter list, host galaxy templates, and dust reddening map to extract spectral measurements from the raw fits. Monte Carlo estimation of the measurement uncertainties of the fitting results can be conducted with the same fitting code. +We provide a brief guide of the Python QSO fitting code (PyQSOFit) to measure spectral properties of SDSS quasars. The code was originally translated from Yue Shen's IDL code to Python. The package includes the main routine, Fe II templates, an input line-fitting parameter list, host galaxy templates, and dust reddening map to extract spectral measurements from the raw fits. Monte Carlo or MCMC estimation of the measurement uncertainties of the fitting results can be conducted with the same fitting code. The code takes an input spectrum (observed-frame wavelength, flux density and error arrays) and the redshift as input parameters, performs the fitting in the restframe, and outputs the best-fit parameters and quality-checking plots to the paths specified by the user. @@ -10,27 +12,22 @@ The code uses an input line-fitting parameter list to specify the fitting range Use this code at your own risk, as we are not responsible for any errors. But if you report bugs, it will be greatly appreciated. -## Install +### Install + +Bleeding edge: + +``git clone https://github.com/legolason/PyQSOFit``
+``cd PyQSOFit``
+``python -m pip install .``
+ +Pip install (stable version): -v1.1 (stable): https://github.com/legolason/PyQSOFit/releases/tag/v1.1 +``pip install pyqsofit`` (coming soon) -## Known problem +### Cite -1. During the line fitting procedure, some emission lines need less Gaussian models than provided to be well fitted. In these circumstances, the code will give two (or more) exactly the same Gaussian models to fit the data instead of one. This problem will not affect the physical measurements but only wierd in the QA image. One can use BIC to judge the proper number of Gaussian models for each line referencing to our `example.ipynb`. -2. Since the host decomposition hiring BC03 template is non-negative linear fitting, the host component will not stay at zero even if no hosts are detected or the decomposition is failed. We suggest user to determine the reliability of the host decomposition through QA image and the host fraction parameters f_host. (i.e., f_host>0.05 from (Shen et al. 2019)[https://doi.org/10.1088/0004-637X/805/2/96]) +Preferred code citation: [Guo, H., Shen, Y., Wang, S. 2018, ascl:1809.008](https://ui.adsabs.harvard.edu/abs/2018ascl). -## Cite this code +Please also cite: [Shen, Y. et al. 2019, ApJS, 241, 34S](https://ui.adsabs.harvard.edu/abs/2019ApJS..241...34S/abstract) -> The preferred citation for this code is Guo, Shen & Wang (2018), ascl:1809:008\ -> @misc{2018ascl.soft09008G,\ -> author = {{Guo}, H. and {Shen}, Y. and {Wang}, S.},\ -> title = "{PyQSOFit: Python code to fit the spectrum of quasars}",\ -> keywords = {Software },\ -> howpublished = {Astrophysics Source Code Library},\ -> year = 2018,\ -> month = sep,\ -> archivePrefix = "ascl",\ -> eprint = {1809.008},\ -> adsurl = {[http://adsabs.harvard.edu/abs/2018ascl.soft09008G}](http://adsabs.harvard.edu/abs/2018ascl.soft09008G%7D),\ -> adsnote = {Provided by the SAO/NASA Astrophysics Data System}\ -> } +If using new host decompistion tools (`host_prior=True`), please cite: [Ren, W. et al. 2024](https://ui.adsabs.harvard.edu/abs/2024arXiv240617598R/abstract) \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..d4bb2cbb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/_build/_sources/index.rst.txt b/docs/_build/_sources/index.rst.txt new file mode 100644 index 00000000..b43b0df7 --- /dev/null +++ b/docs/_build/_sources/index.rst.txt @@ -0,0 +1,20 @@ +.. pyqsofit documentation master file, created by + sphinx-quickstart on Fri Jun 28 18:21:35 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to pyqsofit's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/_build/_sources/modules.rst.txt b/docs/_build/_sources/modules.rst.txt new file mode 100644 index 00000000..84849f95 --- /dev/null +++ b/docs/_build/_sources/modules.rst.txt @@ -0,0 +1,7 @@ +pyqsofit +======== + +.. toctree:: + :maxdepth: 4 + + pyqsofit diff --git a/docs/_build/_sources/pyqsofit.rst.txt b/docs/_build/_sources/pyqsofit.rst.txt new file mode 100644 index 00000000..40a2bca4 --- /dev/null +++ b/docs/_build/_sources/pyqsofit.rst.txt @@ -0,0 +1,45 @@ +pyqsofit package +================ + +Submodules +---------- + +pyqsofit.HostDecomp module +-------------------------- + +.. automodule:: pyqsofit.HostDecomp + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.MESFit module +---------------------- + +.. automodule:: pyqsofit.MESFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.PyQSOFit module +------------------------ + +.. automodule:: pyqsofit.PyQSOFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.version module +----------------------- + +.. automodule:: pyqsofit.version + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: pyqsofit + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/_build/_static/alabaster.css b/docs/_build/_static/alabaster.css new file mode 100644 index 00000000..e3174bf9 --- /dev/null +++ b/docs/_build/_static/alabaster.css @@ -0,0 +1,708 @@ +@import url("basic.css"); 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+} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; 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+ margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: inherit; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/docs/_build/_static/custom.css b/docs/_build/_static/custom.css new file mode 100644 index 00000000..2a924f1d --- /dev/null +++ b/docs/_build/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/docs/_build/_static/doctools.js b/docs/_build/_static/doctools.js new file mode 100644 index 00000000..4d67807d --- /dev/null +++ b/docs/_build/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/docs/_build/_static/documentation_options.js b/docs/_build/_static/documentation_options.js new file mode 100644 index 00000000..44b5d19e --- /dev/null +++ b/docs/_build/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '2.1.6', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/docs/_build/_static/file.png b/docs/_build/_static/file.png new file mode 100644 index 00000000..a858a410 Binary files /dev/null and b/docs/_build/_static/file.png differ diff --git a/docs/_build/_static/language_data.js b/docs/_build/_static/language_data.js new file mode 100644 index 00000000..367b8ed8 --- /dev/null +++ b/docs/_build/_static/language_data.js @@ -0,0 +1,199 @@ +/* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/docs/_build/_static/minus.png b/docs/_build/_static/minus.png new file mode 100644 index 00000000..d96755fd Binary files /dev/null and b/docs/_build/_static/minus.png differ diff --git a/docs/_build/_static/plus.png b/docs/_build/_static/plus.png new file mode 100644 index 00000000..7107cec9 Binary files /dev/null and b/docs/_build/_static/plus.png differ diff --git a/docs/_build/_static/pygments.css b/docs/_build/_static/pygments.css new file mode 100644 index 00000000..07454c6b --- /dev/null +++ b/docs/_build/_static/pygments.css @@ -0,0 +1,83 @@ +pre { line-height: 125%; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/docs/_build/_static/sphinx_highlight.js b/docs/_build/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/docs/_build/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/docs/_build/genindex.html b/docs/_build/genindex.html new file mode 100644 index 00000000..cf5cf573 --- /dev/null +++ b/docs/_build/genindex.html @@ -0,0 +1,410 @@ + + + + + + + Index — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ A + | B + | C + | D + | F + | G + | H + | I + | L + | M + | N + | O + | P + | Q + | R + | S + | T + +
+

A

+ + +
+ +

B

+ + +
+ +

C

+ + + +
+ +

D

+ + + +
+ +

F

+ + + +
+ +

G

+ + + +
+ +

H

+ + +
+ +

I

+ + + +
+ +

L

+ + + +
+ +

M

+ + +
+ +

N

+ + +
+ +

O

+ + +
+ +

P

+ + + +
    +
  • + pyqsofit.HostDecomp + +
  • +
  • + pyqsofit.MESFit + +
  • +
  • + pyqsofit.PyQSOFit + +
  • +
  • + pyqsofit.version + +
  • +
+ +

Q

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + +
+ + + +
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/docs/_build/index.html b/docs/_build/index.html new file mode 100644 index 00000000..585ad815 --- /dev/null +++ b/docs/_build/index.html @@ -0,0 +1,110 @@ + + + + + + + + Welcome to pyqsofit’s documentation! — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Welcome to pyqsofit’s documentation!¶

+
+
+
+
+

Indices and tables¶

+ +
+ + +
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/docs/_build/modules.html b/docs/_build/modules.html new file mode 100644 index 00000000..b7a8a6bd --- /dev/null +++ b/docs/_build/modules.html @@ -0,0 +1,187 @@ + + + + + + + + pyqsofit — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/docs/_build/objects.inv b/docs/_build/objects.inv new file mode 100644 index 00000000..91d732eb Binary files /dev/null and b/docs/_build/objects.inv differ diff --git a/docs/_build/py-modindex.html b/docs/_build/py-modindex.html new file mode 100644 index 00000000..2a5c74dc --- /dev/null +++ b/docs/_build/py-modindex.html @@ -0,0 +1,134 @@ + + + + + + + Python Module Index — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Python Module Index

+ +
+ p +
+ + + + + + + + + + + + + + + + + + + +
 
+ p
+ pyqsofit +
    + pyqsofit.HostDecomp +
    + pyqsofit.MESFit +
    + pyqsofit.PyQSOFit +
    + pyqsofit.version +
+ + +
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/docs/_build/pyqsofit.html b/docs/_build/pyqsofit.html new file mode 100644 index 00000000..a6571102 --- /dev/null +++ b/docs/_build/pyqsofit.html @@ -0,0 +1,702 @@ + + + + + + + + pyqsofit package — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

pyqsofit package¶

+
+

Submodules¶

+
+
+

pyqsofit.HostDecomp module¶

+

# Path : 20230710PyQSOFit/pyqsofit +# File : PriorDecomp.py +# Time :2023/7/27 15:47 +# Author :Wenke Ren +# version :python 3.10 +# Description:Use the PCA data to decompose the spectra with a priori

+
+
+class pyqsofit.HostDecomp.Linear_decomp(wave, flux, err, n_gal, n_qso, path, host_type='PCA', qso_type='global', na_mask=False)¶
+

Bases: object

+
+
+auto_decomp()¶
+
+ +
+
+gal_model(param: list = None, wave=None)¶
+
+ +
+
+qso_model(param: list = None, wave=None)¶
+
+ +
+ +
+
+class pyqsofit.HostDecomp.Prior_decomp(wave, flux, err, n_gal, n_qso, path, host_type='PCA', qso_type='CZBIN1', na_mask=True, fh_ini_list=(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9))¶
+

Bases: object

+
+
+auto_decomp(reg_factor=0.2)¶
+
+ +
+
+cal_model(param: Parameters, wave=None)¶
+
+ +
+
+decompose(reg_factor, init_params, non_negative=False)¶
+
+ +
+
+gal_model(param: list = None, wave=None)¶
+
+ +
+
+initial_params(fh_ini=None)¶
+
+ +
+
+qso_model(param: list = None, wave=None)¶
+
+ +
+
+read_prior(prior_loc, QSO_prior_name='QSO_pp_prior.csv', GAL_prior_name='GAL_pp_prior.csv')¶
+
+ +
+ +
+
+class pyqsofit.HostDecomp.QSO_PCA(template_path, n_template=5, template_name=None)¶
+

Bases: object

+
+
+interp_data(wave_exp)¶
+
+ +
+ +
+
+class pyqsofit.HostDecomp.host_template(template_path, n_template=5, template_type='PCA')¶
+

Bases: object

+
+
+interp_data(wave_exp, broaden: bool = False, shift: float = 0, sigma: float = 0)¶
+

Interpolate the galaxy template and find the interpolation flux at give wavelength. We also provide +broaden methods which allow user to convolve a gaussian core before the interpolation. However, +considering most template are not evenly sampled, we have to interpolate twice if the broaden method +is used, which might introduce more biases. +:param wave_exp: +:param broaden: +:param shift: float, in km/s +:param sigma: float, in km/s +:return:

+
+ +
+ +
+
+pyqsofit.HostDecomp.ppxf_kinematics(wave, flux, err, path, fit_range=(3700, 8300), MC_iter=0)¶
+
+ +
+
+

pyqsofit.MESFit module¶

+
+
+class pyqsofit.MESFit.MESFit(path=None)¶
+

Bases: object

+

Multi-epoch Spectral Fitting program

+
+
+CalLineSN(w, f, line_min, line_max, conti)¶
+
+ +
+
+Calwidth(wave, flux, wv_min, wv_max)¶
+

Return line fwhm and sigma in unit of km/s

+
+ +
+
+Coadd_spec()¶
+
+ +
+
+Plotline(wave, ymin, ymax)¶
+
+ +
+
+corr(w1, f1, err1, w_ref, f_ref, err_ref, wv_min=None, wv_max=None, n=15, plot=True)¶
+
+ +
+
+fixNL(pardata: BinTableHDU = None, fitdata: dict = None)¶
+

For each line group, we fix the line sigma and scale of narrow lines to the results of mean spectra. +:param pardata: +:param fitdata: +:return:

+
+ +
+
+flux2L(flux, z)¶
+

Transfer flux to luminoity assuming a flat Universe

+
+ +
+
+interp(wave, value, z=0.0, fill_value=0.0)¶
+

interprate to standard wavelenth into rest or obs frame

+
+ +
+
+normNL(norm_line_wv=5008.24, path=None, name='normNL', save=True, tol=1e-10)¶
+
+ +
+
+ppxf_host(rest_wv, fx, error, redshift, wv_min=4125, wv_max=5350, plot=None, quiet=False, mask_width=3000)¶
+

fit the host galaxy to get the stellar velocity dispersion.

+
+ +
+
+residuals_norm(p, mean_wv, mean_spec, flux_new)¶
+
+ +
+
+s2f(array)¶
+

string to float

+
+ +
+ +
+
+

pyqsofit.PyQSOFit module¶

+
+
+class pyqsofit.PyQSOFit.QSOFit(lam, flux, err, z, ra=-999, dec=-999, plateid=None, mjd=None, fiberid=None, path=None, and_mask_in=None, or_mask_in=None, wdisp=None)¶
+

Bases: object

+
+
+Balmer_conti(xval, pp)¶
+

Fit the Balmer continuum from the model of Dietrich+02

+
+ +
+
+CalFWHM(logsigma)¶
+

transfer the logFWHM to normal frame

+
+ +
+
+F_poly_conti(xval, pp, x0=3000)¶
+

Fit the continuum with a polynomial component account for the dust reddening with a*X+b*X^2+c*X^3

+

TODO: See if LMFIT’s built-in modeles improved performance and numerical stability +https://lmfit.github.io/lmfit-py/builtin_models.html

+
+ +
+
+Fe_flux_balmer(xval, pp)¶
+

Fit the optical FeII on the continuum from 3686 to 7484 A based on Vestergaard & Wilkes 2001

+
+ +
+
+Fe_flux_mgii(xval, pp)¶
+

Fit the UV FeII component on the continuum from 1200 to 3500 A based on Boroson & Green 1992.

+
+ +
+
+Fit(name=None, nsmooth=1, and_mask=False, or_mask=False, reject_badpix=True, deredden=True, wave_range=None, wave_mask=None, decompose_host=True, host_prior=False, host_prior_scale=0.2, host_line_mask=True, decomp_na_mask=False, qso_type='global', npca_qso=10, host_type='BC03', npca_gal=5, Fe_uv_op=True, poly=False, BC=False, rej_abs_conti=False, rej_abs_line=False, initial_guess=None, n_pix_min_conti=100, param_file_name='qsopar.fits', MC=False, MCMC=False, save_fits_name=None, nburn=20, nsamp=200, nthin=10, epsilon_jitter=0.0, linefit=True, save_result=True, plot_fig=True, save_fits_path='.', save_fig=True, plot_corner=True, verbose=False, kwargs_plot={}, kwargs_conti_emcee={}, kwargs_line_emcee={})¶
+

Fit the QSO spectrum and get different decomposed components and corresponding parameters

+
+

Parameter:¶

+
+
name: str, optional

source name, Default is None. If None, it will use plateid+mjd+fiberid as the name. If there are no +such parameters, it will be empty.

+
+
nsmooth: integer number, optional

do n-pixel smoothing to the raw input flux and err spectra. The default is set to 1 (no smooth). +It will return the same array size. We note that smooth the raw data is not suggested, this function is in case of some fail-fitted low S/N spectra.

+
+
and_mask: bool, optional

If True, and and_mask or or_mask is not None, it will delete the masked pixels, and only return the remained pixels. Default: False

+
+
or_mask: bool, optional

If True, and and_mask or or_mask is not None, it will delete the masked pixels, and only return the remained pixels. Default: False

+
+
reject_badpix: bool, optional

reject 10 most possible outliers by the test of pointDistGESD. One important Caveat here is that this process will also delete narrow emission lines +in some high SN ratio object e.g., [OIII]. Only use it when you are definitely clear about what you are doing. It will return the remained pixels.

+
+
deredden: bool, optional

correct the Galactic extinction only if the RA and Dec are available. It will return the corrected flux with the same array size. Default: True.

+
+
wave_range: 2-element array, optional

trim input wavelength (lam) according to the min and max range of the input 2-element array, e.g., +np.array([4000.,6000.]) in Rest frame range. Default: None

+
+
wave_mask: 2-D array

mask some absorption lines or sky lines in spectrum, e.g., np.array([[2200.,2300.]]), np.array([[5650.,5750.],[5850.,5900.]])

+
+
decompose_host: bool, optional

If True, the host galaxy-QSO decomposition will be applied. If no more than 100 pixels are negative, the result will be applied. The Decomposition is +based on the PCA method of Yip et al. 2004 (AJ, 128, 585) & (128, 2603). Now the template is only available for redshift < 1.16 in specific absolute +magnitude bins. For galaxy, the global model has 10 PCA components and first 5 will enough to reproduce 98.37% galaxy spectra. For QSO, the global model +has 50, and the first 20 will reproduce 96.89% QSOs. If have i-band absolute magnitude, the Luminosity-redshift binned PCA components are available. +Then the first 10 PCA in each bin is enough to reproduce most QSO spectrum. Default: False

+
+
host_prior: bool, optional

This parameter is only useful when the decompose_host is True and BC03 is False. If True, the code will +adopt the prior parameters given in the pca file to perform host decomposition.

+
+
host_prior_scale: float, optional

If the prior decomposition is performed, the code will use this parameter to scale the prior penalty to the +original chi2. Default: 0.2

+
+
host_line_mask: bool, optional

If True, the line region of galaxy will be masked when subtracted from original spectra. Default: True

+
+
BC03: bool, optional

if True, it will use Bruzual1 & Charlot 2003 host model to fit spectrum, high shift host will be low resolution R ~ 300, the rest is R ~ 2000. Default: False

+
+
Mi: float, optional

i-band absolute magnitude. It only works when decompose_host is True. If not None, the Luminosity redshift binned PCA will be used to decompose +the spectrum. Default: None

+
+
npca_gal: int, optional

the number of galaxy PCA components applied. It only works when decompose_host is True. The default is 5, +which is already account for 98.37% galaxies.

+
+
npca_qso: int, optional

the number of QSO PCA components applied. It only works when decompose_host is True. The default is 20, +No matter the global or luminosity-redshift binned PCA is used, it can reproduce > 92% QSOs. The binned PCA +is better if have Mi information.

+
+
Fe_uv_op: bool, optional

if True, fit continuum with UV and optical FeII template. Default: True

+
+
poly: bool, optional

if True, fit continuum with the polynomial component to account for the dust reddening. Default: False

+
+
BC: bool, optional

if True, fit continuum with Balmer continua from 1000 to 3646A. Default: False

+
+
rej_abs_conti: bool, optional

if True, it will iterate the continuum fitting once, rejecting 3 sigma outlier absorption pixels in the continuum +(< 3500A), which might fall into the broad absorption lines. Default: False

+
+
rej_abs_line: bool, optional

if True, it will iterate the emission line fitting twice, rejecting 3 sigma outlier absorption pixels +which might fall into the broad absorption lines. Default: False

+
+
n_pix_min_conti: float, optional

minimum number of negative pixels for host continuuum fit to be rejected. Default: 100

+
+
param_file_name: str, optional

name of the qso fitting parameter FITS file. Default: ‘qsopar.fits’

+
+
MC: bool, optional

if True, do Monte Carlo resampling of the spectrum based on the input error array to produce the MC error array. +if False, the code will not save the MLE minimization error produced by lmfit since it is biased and can not be trusted. +But it can be still output by using the lmfit attribute. Default: False

+
+
MCMC: bool, optional

if True, do Markov Chain Monte Carlo sampling of the posterior probability densities after MLE fitting to produce the error array. +Note: An error will be thrown if both MC and MCMC are True. Default: False

+
+
nburn: int, optional

the number of burn-in samples to run MCMC chain if MCMC=True. It only works when MCMC is True. Default: 20

+
+
nsamp: int, optional

the number of trials of the MC process to produce the error array (if MC=True) or number samples to run MCMC chain (if MCMC=True). Should be larger than 20. It only works when either MC or MCMC is True. Default: 200

+
+
linefit: bool, optional

if True, the emission line will be fitted. Default: True

+
+
save_result: bool, optional

if True, all the fitting results will be saved to a fits file, Default: True

+
+
plot_fig: bool, optional

if True, the fitting results will be plotted. Default: True

+
+
save_fig: bool, optional

if True, the figure will be saved, and the path can be set by “save_fig_pathâ€. Default: True

+
+
plot_corner: bool, optinoal

whether or not to plot the corner plot results if MCMC=True. Default: True

+
+
save_fig_path: str, optional

the output path of the figure. If None, the default “save_fig_path†is set to “pathâ€

+
+
save_fits_path: str, optional

the output path of the result fits. If None, the default “save_fits_path†is set to “pathâ€

+
+
save_fits_name: str, optional

the output name of the result fits. Default: “result.fitsâ€

+
+
verbose: bool, optional

turn on (True) or off (False) debugging output. Default: False

+
+
kwargs_plot: dict, optional

extra aguments for plot_fig for plotting results. See LINK TO PLOT_FIG_DOC. Default: {}

+
+
kwargs_conti_emcee: dict, optional

extra aguments for emcee Sampler for continuum fitting. Default: {}

+
+
kwargs_line_emcee: dict, optional

extra arguments for emcee Sampler for line fitting. Default: {}

+
+
+
+
+

Return:¶

+
+
+

Properties:¶

+
+
.wave: array

the rest wavelength, some pixels have been removed.

+
+
.flux: array

the rest flux. Dereddened and *(1+z) flux.

+
+
.err: array

the error.

+
+
.wave_prereduced: array

the wavelength after removing bad pixels, masking, deredden, spectral trim, and smoothing.

+
+
.flux_prereduced: array

the flux after removing bad pixels, masking, deredden, spectral trim, and smoothing.

+
+
.err_prereduced: array

the error after removing bad pixels, masking, deredden, spectral trim, and smoothing.

+
+
.host: array

the model of host galaxy from PCA method

+
+
.qso: array

the model of a quasar from PCA method.

+
+
.SN_ratio_conti: float

the mean S/N ratio of 1350, 3000 and 5100A.

+
+
.conti_fit.: structure

all the continuum fitting results, including best-fit parameters and Chisquare, etc. For details, +see https://lmfit.github.io/lmfit-py/fitting.html

+
+
.f_conti_model: array

the continuum model including power-law, polynomial, optical/UV FeII, Balmer continuum.

+
+
.f_bc_model: array

the Balmer continuum model.

+
+
.f_fe_uv_model: array

the UV FeII model.

+
+
.f_fe_op_model: array

the optical FeII model.

+
+
.f_pl_model: array

the power-law model.

+
+
.f_poly_model: array

the polynomial model.

+
+
.PL_poly_BC: array

The combination of Powerlaw, polynomial and Balmer continuum model.

+
+
.line_flux: array

the emission line flux after subtracting the .f_conti_model.

+
+
.line_fit: structrue

Line fitting results for last complexes (From Lya to Ha) , including best-fit parameters, errors (lmfit derived) and Chisquare, etc. For details, +see https://lmfit.github.io/lmfit-py/fitting.html

+
+
.gauss_result: array

3*n Gaussian parameters for all lines in the format of [scale, centerwave, sigma ], n is number of Gaussians for all complexes. +ADD UNITS

+
+
gauss_result_all: array

[nsamp, 3*n] Gaussian parameters for all lines in the format of [scale, centerwave, sigma ], n is number of Gaussians for all complexes. +ADD UNITS

+
+
.conti_result: array

continuum parameters, including widely used continuum parameters and monochromatic flux at 1350, 3000 +and 5100 Angstrom, etc. The corresponding names are listed in .conti_result_name. For all continuum fitting results, +go to .conti_fit.params.

+
+
.conti_result_name: array

the names for .conti_result.

+
+
.fur_result: array

emission line parameters, including FWHM, sigma, EW, measured from whole model of each main broad emission line covered. +The corresponding names are listed in .line_result_name.

+
+
.fur_result_name: array

the names for .fur_result.

+
+
.line_result: array

emission line parameters, including FWHM, sigma, EW, measured from whole model of each main broad emission line covered, +and fitting parameters of each Gaussian component. The corresponding names are listed in .line_result_name.

+
+
.line_result_name: array

the names for .line_result.

+
+
.uniq_linecomp_sort: array

the sorted complex names.

+
+
.all_comp_range: array

the start and end wavelength for each complex. e.g., Hb is [4640. 5100.] AA.

+
+
.linelist: array

the information listed in the param_file_name (qsopar.fits).

+
+
+
+
+ +
+
+Get_Fe_flux(ranges, pp=None)¶
+

Calculate the flux of fitted FeII template within given wavelength ranges. +ranges: 1-D array, 2-D array

+
+

if 1-D array was given, it should contain two parameters contain a range of wavelength. FeII flux within this range would be calculate and documented in the result fits file. +if 2-D array was given, it should contain a series of ranges. FeII flux within these ranges would be documented respectively.

+
+
+
pp: 1-D array with 3 or 6 items.

If 3 parameters were given, function will choose a proper template (MgII or balmer) according to the range. +If the range give excess either template, an error would be arose. +If 6 parameters were given (recommended), function would adopt the first three for the MgII template and the last three for the balmer.

+
+
+
+ +
+
+Manygauss(xval, pp)¶
+

Robust function for multi-Gaussian model used to fit the emission lines

+

This is evaluated many times within the scipy optimize, so we want to keep the code as fast as possible +Hence, it is vectorized so pp must have shape [ngauss, 3]

+

xval: wavelength array in AA

+
+
pp: Paramaters [ngauss*3]

scale: line amplitude +wave: central ln wavelength in AA +sigma: width in km/s

+
+
+
+ +
+
+Onegauss(xval, pp)¶
+

The single Gaussian model used to fit the emission lines +Parameter: the scale factor, central wavelength in logwave, line FWHM in logwave

+

This is evaluated many times within the scipy optimize, so we want to keep the code as fast as possible +Hence, we avoid calling any external libraries like astropy’s Gaussian here

+

It is slightly faster to fit the (un-normalized) amplitude directly to avoid blow-up at small sigma

+

xval: wavelength array in AA

+

TODO: See if LMFIT’s built-in modeles improved performance +https://lmfit.github.io/lmfit-py/builtin_models.html

+
+
pp: Paramaters [3]

scale: line amplitude +wave: central ln wavelength in AA +sigma: width in km/s

+
+
+
+ +
+
+PL(xval, pp, x0=3000)¶
+
+ +
+
+Smooth(y, box_pts)¶
+

Smooth the flux with n pixels

+
+ +
+
+decompose_host_qso(wave, flux, err, path)¶
+

Decompose the host galaxy from QSO

+
+ +
+
+fit_continuum(wave, flux, err, ra, dec, plateid, mjd, fiberid)¶
+

Fit the continuum with PL, Polynomial, UV/optical FeII, Balmer continuum

+
+

Parameter:¶

+
+
lam: array, required

wavelength

+
+
flux: array, required

flux

+
+
err: array, required

1 sigma error

+
+
conti_windows: 2d array, optional

Continuum fitting windows. If None, use default windows. For special situations, you +may need to change these to improve the fitting (e.g., Ly-alpha absorption troughs, etc.) Default: None

+
+
+
+
+

Return:¶

+
+
+ +
+
+fit_lines(wave, line_flux, err, f)¶
+

Fit the emission lines with Gaussian profiles

+
+ +
+
+flux2L(flux, z=None)¶
+

Transfer flux to luminoity assuming a flat Universe

+
+ +
+
+line_prop(compcenter, pp, linetype='broad', ln_sigma_br=0.0017)¶
+

Calculate the further results for the broad component in emission lines, e.g., FWHM, sigma, peak, line flux +The compcenter is the theortical vacuum wavelength for the broad compoenet. +compcenter: +pp: +linetype: ‘broad’ or ‘narrow’ +ln_sigma_br: line sigma separating broad and narrow lines (AA??) +ln_sigma_max: Max sigma to consider in the calculation (used to exclude ultra-broad wings, etc.)

+
+ +
+
+line_prop_from_name(line_name, line_type='broad', sample_index=-1, ln_sigma_br=0.0017)¶
+

line_name: line name e.g., ‘Ha_br’

+
+ +
+
+plot_fig(save_fig_path='.', broad_fwhm=1200, plot_line_name=True, plot_legend=True, ylims=None, plot_residual=True, show_title=True, plot_br_prop=False)¶
+

Plot the results

+
+
broad_fwhm: float, optional

Definition for width of the broad lines. Default: 1200 km/s (careful, is not the exact separation used in line_prop)

+
+
plot_line_name: bool, optional

if True, serval main emission lines will be plotted in the first panel of the output figure. Default: False

+
+
+

TODO: Consider splitting up into plot_conti and plot_complex functions +Wenke: I totally agree with that!!! +to encourage flexibility/reuse

+
+ +
+
+read_out_params(param_file_path='qsopar.fits')¶
+
+ +
+
+save_result(conti_result, conti_result_type, conti_result_name, line_result, line_result_type, line_result_name, save_fits_path, save_fits_name)¶
+

Save all data to fits

+
+ +
+
+set_mpl_style(tsize=18, tdir='in', major=5.0, minor=3.0, lwidth=1.8, lhandle=2.0)¶
+

Function to set MPL style

+
+ +
+
+to_Spectrum1D()¶
+
+ +
+ +
+
+pyqsofit.PyQSOFit.get_err(s, margin=0.16, axis=0, default_value=-1.0)¶
+

Get 100*margin percent distribution of a given data. +:param s: 1-D array or 2-D array. If a 1-D array is given, the data will deem the array as the data sample and the +axis parameter will be ignored. If a 2-D array is given, how the function deel with this data will depend on the +axis. If axis==0, the function will calculate the distribution of each column of the array. If axis==1, the +function will calculate the distribution of each row of the array. +:param margin: The margin of the distribution. The default value is 16%, which means the function will calculate +about 1 sigma error for each sample +:param axis: How the function deel with the data, see above. +:return: float or 1-D array, depends on the input data.

+
+ +
+
+pyqsofit.PyQSOFit.read_conti_params(param_file_path='qsopar.fits')¶
+
+ +
+
+pyqsofit.PyQSOFit.read_line_params(param_file_path='qsopar.fits')¶
+
+ +
+
+

pyqsofit.version module¶

+
+
+

Module contents¶

+
+
+ + +
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/docs/_build/search.html b/docs/_build/search.html new file mode 100644 index 00000000..0d656742 --- /dev/null +++ b/docs/_build/search.html @@ -0,0 +1,116 @@ + + + + + + + Search — pyqsofit 2.1.6 documentation + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Search

+ + + + +

+ Searching for multiple words only shows matches that contain + all words. +

+ + +
+ + + +
+ + +
+ + +
+ +
+
+ +
+
+ + + + + + + \ No newline at end of file diff --git a/docs/builddocs b/docs/builddocs new file mode 100644 index 00000000..87a07bc3 --- /dev/null +++ b/docs/builddocs @@ -0,0 +1 @@ +sphinx-build docs docs/_build diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 00000000..75fb5c0b --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,32 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +import os +import sys +sys.path.insert(0, os.path.abspath('..')) + +project = 'pyqsofit' +copyright = '2024, Hengxiao Guo' +author = 'Hengxiao Guo' +release = '2.1.6' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = ['sphinx.ext.autodoc'] + +templates_path = ['_templates'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'alabaster' +html_static_path = ['_static'] diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 00000000..b43b0df7 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,20 @@ +.. pyqsofit documentation master file, created by + sphinx-quickstart on Fri Jun 28 18:21:35 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to pyqsofit's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..32bb2452 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/modules.rst b/docs/modules.rst new file mode 100644 index 00000000..84849f95 --- /dev/null +++ b/docs/modules.rst @@ -0,0 +1,7 @@ +pyqsofit +======== + +.. toctree:: + :maxdepth: 4 + + pyqsofit diff --git a/docs/pyqsofit.rst b/docs/pyqsofit.rst new file mode 100644 index 00000000..40a2bca4 --- /dev/null +++ b/docs/pyqsofit.rst @@ -0,0 +1,45 @@ +pyqsofit package +================ + +Submodules +---------- + +pyqsofit.HostDecomp module +-------------------------- + +.. automodule:: pyqsofit.HostDecomp + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.MESFit module +---------------------- + +.. automodule:: pyqsofit.MESFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.PyQSOFit module +------------------------ + +.. automodule:: pyqsofit.PyQSOFit + :members: + :undoc-members: + :show-inheritance: + +pyqsofit.version module +----------------------- + +.. automodule:: pyqsofit.version + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: pyqsofit + :members: + :undoc-members: + :show-inheritance: diff --git a/example/example.ipynb b/example/example.ipynb index 3083601a..7b1e41b8 100644 --- a/example/example.ipynb +++ b/example/example.ipynb @@ -6,7 +6,7 @@ "source": [ "![alt text][logo]\n", "\n", - "[logo]: https://github.com/legolason/PyQSOFit/blob/master/pyqsofit/QSOFit_logo.png?raw=true\n", + "[logo]: https://github.com/legolason/PyQSOFit/blob/master/src/pyqsofit/QSOFit_logo.png?raw=true\n", "\n", "\n", "# PyQSOFit\n", @@ -45,7 +45,7 @@ "2) [pandas](https://pandas.pydata.org/)
\n", "3) [corner](https://corner.readthedocs.io/en/latest/)
\n", "\n", - "If using pPXF to get the host component (`use_ppxf=True`),\n", + "To get the pPXF host model and gas kinematics,\n", "\n", "1) [pPXF](https://pypi.org/project/ppxf/)\n", "\n", @@ -67,26 +67,26 @@ "## Possible future updates\n", "1) Option for using Gauss-Hermite profile to fit the emission lines.
\n", "2) Simultaneously fit several epochs for the same source since the time domain era is coming.
\n", - "3) Add functions to fit the absorption lines.
\n", - "4) Produce more secondary parameters from spectral fitting.
\n", - "5) Speed up the code by e.g., choosing better initial conditions (especially for the continuum and narrow-line flux normalizations).
\n", - "6) Option for automatically determining the number of broad emission line components to include in a fit using e.g., BIC. This will take longer to execute initially but might make the MCMC sampling faster and fits more reliable if fewer components are used, especially for low S/N or BAL quasar spectra.
\n", - "7) Improved integration with pPXF, specutils, etc.
\n", - "8) Better code documentation.
\n", + "3) Produce more secondary parameters from spectral fitting.
\n", + "4) Speed up the code by e.g., choosing better initial conditions (especially for the continuum and narrow-line flux normalizations).
\n", + "especially for low S/N or BAL quasar spectra.
\n", + "5) Improved integration with pPXF, specutils, etc.
\n", + "6) Better code documentation.
\n", "\n", "\n", "## Authors\n", "[Hengxiao Guo](https://hengxiaoguo.wixsite.com/hengxiaoguo), hengxiaoguo AT gmail.com (SHAO)
\n", "[Yue Shen](http://quasar.astro.illinois.edu/), shenyue AT illinois.edu (UIUC)
\n", "Shu Wang, wangshukiaa AT pku.edu.cn (Seoul National University)
\n", - "[Colin J. Burke](https://burke86.github.io/), colinjb2 AT illinois.edu (UIUC)
\n", + "[Colin J. Burke](https://burke86.github.io/), colin.j.burke AT yale.edu (Yale)
\n", "[Wenke Ren](https://github.com/WenkeRen/), rwk AT mail.ustc.edu.cn (USTC)
\n", "\n", "\n", "## Acknowledgement\n", "If our code makes your life easier, it would be appreciated to cite us:
\n", "1) [Guo, H., Shen, Y., Wang, S. 2018, ascl:1809.008](https://ui.adsabs.harvard.edu/abs/2018ascl.soft09008G/abstract)\n", - "2) [Shen, Y. et al., ApJS, 241, 34S](http://adsabs.harvard.edu/abs/2018arXiv181001447S)\n" + "2) [Shen, Y. et al., ApJS, 241, 34S](http://adsabs.harvard.edu/abs/2018arXiv181001447S)\n", + "3) [Ren, W. et al. 2024](https://ui.adsabs.harvard.edu/abs/2024arXiv240617598R/abstract)\n" ] }, { diff --git a/pyqsofit/qsopar.fits b/pyqsofit/qsopar.fits deleted file mode 100644 index 54152239..00000000 --- a/pyqsofit/qsopar.fits +++ /dev/null @@ -1,22 +0,0 @@ -SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 88 / length of dimension 1 NAXIS2 = 17 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 14 / number of table fields LAMBDA = 'Vacuum Wavelength in Ang' MINWAV = 'Lower complex fitting wavelength range' MAXWAV = 'Upper complex fitting wavelength range' NGAUSS = 'Number of Gaussians for the line' INISIG = 'Initial guess of linesigma [in lnlambda]' MINSIG = 'Lower range of line sigma [lnlambda]' MAXSIG = 'Upper range of line sigma [lnlambda]' VOFF = 'Limits on velocity offset from the central wavelength [lnlambda]' VINDEX = 'Entries w/ same NONZERO vindex constrained to have same velocity' WINDEX = 'Entries w/ same NONZERO windex constrained to have same width' FINDEX = 'Entries w/ same NONZERO findex have constrained flux ratios' FVALUE = 'Relative scale factor for entries w/ same findex' EXTNAME = 'DATA ' / extension name TTYPE1 = 'lambda ' TFORM1 = 'E ' TTYPE2 = 'compname' TFORM2 = '20A ' TTYPE3 = 'minwav ' TFORM3 = 'E ' TTYPE4 = 'maxwav ' TFORM4 = 'E ' TTYPE5 = 'linename' TFORM5 = '20A ' TTYPE6 = 'ngauss ' TFORM6 = 'E ' TTYPE7 = 'inisig ' TFORM7 = 'E ' TTYPE8 = 'minsig ' TFORM8 = 'E ' TTYPE9 = 'maxsig ' TFORM9 = 'E ' TTYPE10 = 'voff ' TFORM10 = 'E ' TTYPE11 = 'vindex ' TFORM11 = 'E ' TTYPE12 = 'windex ' TFORM12 = 'E ' TTYPE13 = 'findex ' TFORM13 = 'E ' TTYPE14 = 'fvalue ' TFORM14 = 'E ' END EÍ$áHaEÈEÔ€Ha_br@@;£× -;ƒo=LÌÍ= lower) & (xval <= upper)], xval[(xval >= lower) & (xval <= upper)]) + flux = integrate.trapezoid(yval[(xval >= lower) & (xval <= upper)], xval[(xval >= lower) & (xval <= upper)]) return flux def read_out_params(self, param_file_path='qsopar.fits'): diff --git a/pyqsofit/QSOFit_logo.png b/src/pyqsofit/QSOFit_logo.png similarity index 100% rename from pyqsofit/QSOFit_logo.png rename to src/pyqsofit/QSOFit_logo.png diff --git a/pyqsofit/__init__.py b/src/pyqsofit/__init__.py similarity index 100% rename from pyqsofit/__init__.py rename to src/pyqsofit/__init__.py diff --git a/pyqsofit/bc03/10_cst_6gyr_z02.spec.gz b/src/pyqsofit/bc03/10_cst_6gyr_z02.spec.gz similarity index 100% rename from pyqsofit/bc03/10_cst_6gyr_z02.spec.gz rename to 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src/pyqsofit/pca/prior/GAL_pp_prior.csv diff --git a/pyqsofit/pca/prior/QSO_pp_prior_CZBIN1.csv b/src/pyqsofit/pca/prior/QSO_pp_prior_CZBIN1.csv similarity index 100% rename from pyqsofit/pca/prior/QSO_pp_prior_CZBIN1.csv rename to src/pyqsofit/pca/prior/QSO_pp_prior_CZBIN1.csv diff --git a/pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv b/src/pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv similarity index 100% rename from pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv rename to src/pyqsofit/pca/prior/QSO_pp_prior_DZBIN1.csv diff --git a/src/pyqsofit/qsopar.fits b/src/pyqsofit/qsopar.fits new file mode 100644 index 00000000..9f37b21b --- /dev/null +++ b/src/pyqsofit/qsopar.fits @@ -0,0 +1,26 @@ +SIMPLE = T / conforms to FITS standard BITPIX = 8 / array data type NAXIS = 0 / number of array dimensions EXTEND = T AUTHOR = 'Hengxiao Guo' END XTENSION= 'BINTABLE' / binary table extension BITPIX = 8 / array data type NAXIS = 2 / number of array dimensions NAXIS1 = 104 / length of dimension 1 NAXIS2 = 17 / length of dimension 2 PCOUNT = 0 / number of group parameters GCOUNT = 1 / number of groups TFIELDS = 18 / number of table fields TTYPE1 = 'lambda ' TFORM1 = 'E ' TTYPE2 = 'compname' TFORM2 = '20A ' TTYPE3 = 'minwav ' TFORM3 = 'E ' TTYPE4 = 'maxwav ' TFORM4 = 'E ' TTYPE5 = 'linename' TFORM5 = '20A ' TTYPE6 = 'ngauss ' TFORM6 = 'J ' TTYPE7 = 'inisca ' TFORM7 = 'E ' TTYPE8 = 'minsca ' TFORM8 = 'E ' TTYPE9 = 'maxsca ' TFORM9 = 'E ' TTYPE10 = 'inisig ' TFORM10 = 'E ' TTYPE11 = 'minsig ' TFORM11 = 'E ' TTYPE12 = 'maxsig ' TFORM12 = 'E ' TTYPE13 = 'voff ' TFORM13 = 'E ' TTYPE14 = 'vindex ' TFORM14 = 'J ' TTYPE15 = 'windex ' TFORM15 = 'J ' TTYPE16 = 'findex ' TFORM16 = 'J ' TTYPE17 = 'fvalue ' TFORM17 = 'E ' TTYPE18 = 'vary ' TFORM18 = 'J ' EXTNAME = 'LINE_PRIORS' / extension name END EÍ$áHaEÈEÔ€Ha_br=ÌÌÍPù;£× +;ƒo=LÌÍ=0.4.7 +pandas \ No newline at end of file diff --git a/tests/test_dr7sample.py b/tests/test_dr7sample.py new file mode 100644 index 00000000..26e4ee13 --- /dev/null +++ b/tests/test_dr7sample.py @@ -0,0 +1,417 @@ +import glob, os,sys,timeit +import matplotlib +import numpy as np +from astropy.io import fits +import matplotlib.pyplot as plt +import warnings +import matplotlib.backends.backend_pdf as bpdf + +from astroquery.sdss import SDSS +from astropy import coordinates as coords + +from astropy.table import Table + +warnings.filterwarnings("ignore") + + +# Show the versions so we know what works +import astropy +import lmfit +import pyqsofit +print(astropy.__version__) +print(lmfit.__version__) +print(pyqsofit.__version__) + +from pyqsofit.PyQSOFit import QSOFit + +import emcee # optional, for MCMC +print(emcee.__version__) + +def test_dr7(nqsofit=20): + + # Use custom matplotlib style to make Yue happy + QSOFit.set_mpl_style() + + path_ex = os.path.abspath('.') # The absolute path to the example directory + + print(path_ex) + # Setup the parameter file + + # create a header + hdr0 = fits.Header() + hdr0['Author'] = 'Hengxiao Guo' + primary_hdu = fits.PrimaryHDU(header=hdr0) + + """ + Create parameter file + lambda complexname minwav maxwav linename ngauss inisca minsca maxsca inisig minsig maxsig voff vindex windex findex fvalue vary + """ + + line_priors = np.rec.array([ + (6564.61, r'Ha', 6400, 6800, 'Ha_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), + (6564.61, r'Ha', 6400, 6800, 'Ha_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + (6549.85, r'Ha', 6400, 6800, 'NII6549', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.001, 1), + (6585.28, r'Ha', 6400, 6800, 'NII6585', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 1, 0.003, 1), + (6718.29, r'Ha', 6400, 6800, 'SII6718', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), + (6732.67, r'Ha', 6400, 6800, 'SII6732', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 5e-3, 1, 1, 2, 0.001, 1), + + (4862.68, r'Hb', 4640, 5100, 'Hb_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.01, 0, 0, 0, 0.01 , 1), + (4862.68, r'Hb', 4640, 5100, 'Hb_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + (4960.30, r'Hb', 4640, 5100, 'OIII4959c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + (5008.24, r'Hb', 4640, 5100, 'OIII5007c', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.01, 1, 1, 0, 0.004, 1), + #(4960.30, r'Hb', 4640, 5100, 'OIII4959w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.001, 1), + #(5008.24, r'Hb', 4640, 5100, 'OIII5007w', 1, 0.1, 0.0, 1e10, 3e-3, 2.3e-4, 0.004, 0.01, 2, 2, 0, 0.002, 1), + #(4687.02, r'Hb', 4640, 5100, 'HeII4687_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.005, 0, 0, 0, 0.001, 1), + #(4687.02, r'Hb', 4640, 5100, 'HeII4687_na', 1, 0.1, 0.0, 1e10, 1e-3, 2.3e-4, 0.0017, 0.005, 1, 1, 0, 0.001, 1), + + #(3934.78, 'CaII', 3900, 3960, 'CaII3934' , 2, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 99, 0, 0, -0.001, 1), + + #(3728.48, 'OII', 3650, 3800, 'OII3728', 1, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 1, 1, 0, 0.001, 1), + + #(3426.84, 'NeV', 3380, 3480, 'NeV3426', 1, 0.1, 0.0, 1e10, 1e-3, 3.333e-4, 0.0017, 0.01, 0, 0, 0, 0.001, 1), + #(3426.84, 'NeV', 3380, 3480, 'NeV3426_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.01, 0, 0, 0, 0.001, 1), + + (2798.75, 'MgII', 2700, 2900, 'MgII_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.0017, 0, 0, 0, 0.05, 1), + (2798.75, 'MgII', 2700, 2900, 'MgII_na', 2, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + + (1908.73, 'CIII', 1700, 1970, 'CIII_br', 2, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 99, 0, 0, 0.01, 1), + #(1908.73, 'CIII', 1700, 1970, 'CIII_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + #(1892.03, 'CIII', 1700, 1970, 'SiIII1892', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.003, 1, 1, 0, 0.005, 1), + #(1857.40, 'CIII', 1700, 1970, 'AlIII1857', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.003, 1, 1, 0, 0.005, 1), + #(1816.98, 'CIII', 1700, 1970, 'SiII1816', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.0002, 1), + #(1786.7, 'CIII', 1700, 1970, 'FeII1787', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.0002, 1), + #(1750.26, 'CIII', 1700, 1970, 'NIII1750', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + #(1718.55, 'CIII', 1700, 1900, 'NIV1718', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + + (1549.06, 'CIV', 1500, 1700, 'CIV_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.015, 0, 0, 0, 0.05 , 1), + (1549.06, 'CIV', 1500, 1700, 'CIV_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 1, 1, 0, 0.002, 1), + #(1640.42, 'CIV', 1500, 1700, 'HeII1640', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.008, 1, 1, 0, 0.002, 1), + #(1663.48, 'CIV', 1500, 1700, 'OIII1663', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.008, 1, 1, 0, 0.002, 1), + #(1640.42, 'CIV', 1500, 1700, 'HeII1640_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.008, 1, 1, 0, 0.002, 1), + #(1663.48, 'CIV', 1500, 1700, 'OIII1663_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.0025, 0.02, 0.008, 1, 1, 0, 0.002, 1), + + #(1402.06, 'SiIV', 1290, 1450, 'SiIV_OIV1', 1, 0.1, 0.0, 1e10, 5e-3, 0.002, 0.05, 0.015, 1, 1, 0, 0.05, 1), + #(1396.76, 'SiIV', 1290, 1450, 'SiIV_OIV2', 1, 0.1, 0.0, 1e10, 5e-3, 0.002, 0.05, 0.015, 1, 1, 0, 0.05, 1), + #(1335.30, 'SiIV', 1290, 1450, 'CII1335', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + #(1304.35, 'SiIV', 1290, 1450, 'OI1304', 1, 0.1, 0.0, 1e10, 2e-3, 0.001, 0.015, 0.01, 1, 1, 0, 0.001, 1), + + (1215.67, 'Lya', 1150, 1290, 'Lya_br', 1, 0.1, 0.0, 1e10, 5e-3, 0.004, 0.05, 0.02, 0, 0, 0, 0.05 , 1), + (1215.67, 'Lya', 1150, 1290, 'Lya_na', 1, 0.1, 0.0, 1e10, 1e-3, 5e-4, 0.0017, 0.01, 0, 0, 0, 0.002, 1)], + + formats = 'float32, a20, float32, float32, a20, int32, float32, float32, float32, float32, float32, float32, float32, int32, int32, int32, float32, int32', + names = ' lambda, compname, minwav, maxwav, linename, ngauss, inisca, minsca, maxsca, inisig, minsig, maxsig, voff, vindex, windex, findex, fvalue, vary') + + # Header + hdr = fits.Header() + hdr['lambda'] = 'Vacuum Wavelength in Ang' + hdr['minwav'] = 'Lower complex fitting wavelength range' + hdr['maxwav'] = 'Upper complex fitting wavelength range' + hdr['ngauss'] = 'Number of Gaussians for the line' + + # Can be set to negative for absorption lines if you want + hdr['inisca'] = 'Initial guess of line scale [in ??]' + hdr['minsca'] = 'Lower range of line scale [??]' + hdr['maxsca'] = 'Upper range of line scale [??]' + + hdr['inisig'] = 'Initial guess of linesigma [in lnlambda]' + hdr['minsig'] = 'Lower range of line sigma [lnlambda]' + hdr['maxsig'] = 'Upper range of line sigma [lnlambda]' + + hdr['voff '] = 'Limits on velocity offset from the central wavelength [lnlambda]' + hdr['vindex'] = 'Entries w/ same NONZERO vindex constrained to have same velocity' + hdr['windex'] = 'Entries w/ same NONZERO windex constrained to have same width' + hdr['findex'] = 'Entries w/ same NONZERO findex have constrained flux ratios' + hdr['fvalue'] = 'Relative scale factor for entries w/ same findex' + + hdr['vary'] = 'Whether or not to vary the line parameters (set to 0 to fix the line parameters to initial values)' + + # Save line info + hdu1 = fits.BinTableHDU(data=line_priors, name='line_priors') + + """ + In this table, we specify the windows and priors / initial conditions and boundaries for the continuum fitting parameters. + """ + conti_windows = np.rec.array([ + (1150., 1170.), + (1275., 1290.), + (1350., 1360.), + (1445., 1465.), + (1690., 1705.), + (1770., 1810.), + (1970., 2400.), + (2480., 2675.), + (2925., 3400.), + (3775., 3832.), + (4000., 4050.), + (4200., 4230.), + (4435., 4640.), + (5100., 5535.), + (6005., 6035.), + (6110., 6250.), + (6800., 7000.), + (7160., 7180.), + (7500., 7800.), + (8050., 8150.), # Continuum fitting windows (to avoid emission line, etc.) [AA] + ], + formats = 'float32, float32', + names = 'min, max') + + hdu2 = fits.BinTableHDU(data=conti_windows, name='conti_windows') + + conti_priors = np.rec.array([ + ('Fe_uv_norm', 0.0, 0.0, 1e10, 1), # Normalization of the MgII Fe template [flux] + ('Fe_uv_FWHM', 3000, 1200, 18000, 1), # FWHM of the MgII Fe template [AA] + ('Fe_uv_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the MgII Fe template [lnlambda] + ('Fe_op_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Hbeta/Halpha Fe template [flux] + ('Fe_op_FWHM', 3000, 1200, 18000, 1), # FWHM of the Hbeta/Halpha Fe template [AA] + ('Fe_op_shift', 0.0, -0.01, 0.01, 1), # Wavelength shift of the Hbeta/Halpha Fe template [lnlambda] + ('PL_norm', 1.0, 0.0, 1e10, 1), # Normalization of the power-law (PL) continuum f_lambda = (lambda/3000)^-alpha + ('PL_slope', -1.5, -5.0, 3.0, 1), # Slope of the power-law (PL) continuum + ('Blamer_norm', 0.0, 0.0, 1e10, 1), # Normalization of the Balmer continuum at < 3646 AA [flux] (Dietrich et al. 2002) + ('Balmer_Te', 15000, 10000, 50000, 1), # Te of the Balmer continuum at < 3646 AA [K?] + ('Balmer_Tau', 0.5, 0.1, 2.0, 1), # Tau of the Balmer continuum at < 3646 AA + ('conti_a_0', 0.0, None, None, 1), # 1st coefficient of the polynomial continuum + ('conti_a_1', 0.0, None, None, 1), # 2nd coefficient of the polynomial continuum + ('conti_a_2', 0.0, None, None, 1), # 3rd coefficient of the polynomial continuum + # Note: The min/max bounds on the conti_a_0 coefficients are ignored by the code, + # so they can be determined automatically for numerical stability. + ], + + formats = 'a20, float32, float32, float32, int32', + names = 'parname, initial, min, max, vary') + + hdr3 = fits.Header() + hdr3['ini'] = 'Initial guess of line scale [flux]' + hdr3['min'] = 'FWHM of the MgII Fe template' + hdr3['max'] = 'Wavelength shift of the MgII Fe template' + + hdr3['vary'] = 'Whether or not to vary the parameter (set to 0 to fix the continuum parameter to initial values)' + + + hdu3 = fits.BinTableHDU(data=conti_priors, header=hdr3, name='conti_priors') + + """ + In this table, we allow user to customized some key parameters in our result measurements. + """ + + measure_info = Table( + [ + [[1350, 1450, 3000, 4200, 5100]], + [[ + # [2240, 2650], + [4435, 4685], + ]] + ], + names=([ + 'cont_loc', + 'Fe_flux_range' + ]), + dtype=([ + 'float32', + 'float32' + ]) + ) + hdr4 = fits.Header() + hdr4['cont_loc'] = 'The wavelength of continuum luminosity in results' + hdr4['Fe_flux_range'] = 'Fe emission wavelength range calculated in results' + + hdu4 = fits.BinTableHDU(data=measure_info, header=hdr4, name='measure_info') + + # Save line info + hdu_list = fits.HDUList([primary_hdu, hdu1, hdu2, hdu3, hdu4]) + hdu_list.writeto(os.path.join(path_ex, 'qsopar.fits'), overwrite=True) + print('Saving to ', os.path.join(path_ex, 'qsopar.fits')) + + # Download the SDSS DR7 sample + import urllib.request + import gzip + + print('Retrieving DR7 catalog.') + + cat_file_name = 'dr7_bh_Nov19_2013.fits.gz' + + if not os.path.exists(cat_file_name): + urllib.request.urlretrieve(f'http://quasar.astro.illinois.edu/BH_mass/data/catalogs/{cat_file_name}', cat_file_name) + + # Line properties + line_calc_names = ['CIV_br', 'MgII_br', 'Hb_br'] + line_shen_names = ['CIV', 'BROAD_MGII', 'BROAD_HB'] + line_fwhms = np.zeros((nqsofit, len(line_calc_names))) + line_Ls = np.zeros((nqsofit, len(line_calc_names))) + Mis = np.zeros(nqsofit) + zs = np.zeros(nqsofit) + + start = timeit.default_timer() + + with gzip.open(cat_file_name, 'rb') as f: + + spec_all = fits.open(f) + + len_specs = len(spec_all[1].data) + range_rand = np.random.choice(range(len_specs), nqsofit, replace=False) + + #print(spec_all.info()) + #print(repr(spec_all[1].header)) + + # Catalog properties + Mi_all = spec_all[1].data['MI_Z2'] + z_all = spec_all[1].data['REDSHIFT'] + line_fwhm_all = np.zeros_like(line_fwhms) + line_L_all = np.zeros_like(line_Ls) + + # Emission line loop + for j, line in enumerate(line_shen_names): + line_fwhm_all[:,j] = spec_all[1].data[f'FWHM_{line}'][range_rand] + line_L_all[:,j] = spec_all[1].data[f'LOGL_{line}'][range_rand] + + # Save as single PDF + with bpdf.PdfPages(os.path.join(path_ex, 'fit_results.pdf')) as pdf: + + # For each spectrum + for i, ind in enumerate(range_rand): + + plate = spec_all[1].data['PLATE'][ind] + mjd = spec_all[1].data['MJD'][ind] + fiber = spec_all[1].data['FIBER'][ind] + ra = spec_all[1].data['RA'][ind] + dec = spec_all[1].data['DEC'][ind] + Mi = spec_all[1].data['MI_Z2'][ind] + + # Query the spectrum + pos = coords.SkyCoord(ra, dec, unit='deg') + xid = SDSS.query_region(pos, spectro=True, radius='5 arcsec') + + if xid is None: + continue + + mask = (xid['plate'] == plate) & (xid['mjd'] == mjd) & (xid['fiberID'] == fiber) + print(xid[mask]) + + if len(xid[mask]) < 1: + print('No spectrum found.') + return + + sp = SDSS.get_spectra(matches=xid[mask]) + print(sp) + + if len(sp) < 1: + print('No spectrum found.') + return + + data = sp[0] + + # Requried + lam = 10**data[1].data['loglam'] # OBS wavelength [A] + flux = data[1].data['flux'] # OBS flux [erg/s/cm^2/A] + err = 1/np.sqrt(data[1].data['ivar']) # 1 sigma error + z = data[2].data['z'][0] # Redshift + + q = QSOFit(lam, flux, err, z, ra=ra, dec=dec, plateid=plate, mjd=mjd, fiberid=fiber, path=path_ex) + + # Do the fitting + q.Fit(param_file_name='qsopar.fits', name=None, qso_type='global', host_type='BC03', save_fig=False, save_result=False) + + # Test with host prior + q.Fit(param_file_name='qsopar.fits', name=None, host_prior=True, qso_type='global', host_type='PCA', save_fig=False, save_result=False) + + # Emission line loop + for j, line in enumerate(line_calc_names): + + print(line) + + if line.endswith('_br'): + line_type = 'broad' + else: + line_type = 'narrow' + + # Get the line properties + fwhm, sigma, ew, peak, area, snr = q.line_prop_from_name(line, line_type) + + print(f"Broad {line}:") + print("FWHM (km/s)", np.round(fwhm, 1)) + print("Sigma (km/s)", np.round(sigma, 1)) + print("EW (A)", np.round(ew, 1)) + print("Peak (A)", np.round(peak, 1)) + print("area (10^(-17) erg/s/cm^2)", np.round(area, 1)) + print("") + + line_fwhms[i, j] = fwhm + line_Ls[i, j] = np.log10(q.flux2L(area)) + Mis[i] = Mi + zs[i] = z + + + # Stack the results into 1 file + #pdf.savefig(q.fig) # Turn this off for github actions + + # End open file + + # Summary figures + + def rmse(predictions, targets): + predictions = np.array(predictions) + targets = np.array(targets) + return np.sqrt(((predictions - targets)**2).mean()) + + fig, ax = plt.subplots(1, 1, figsize=(8,5)) + ax.scatter(z_all, Mi_all, color='k', marker='.', alpha=0.01) + ax.scatter(zs, Mis, color='r', marker='o', alpha=0.5) + ax.set_title(pyqsofit.__version__) + + ax.set_xlabel('Redshift', fontsize=20) + ax.set_ylabel(r'$M_i(z=2)$', fontsize=20) + + ax.set_xlim([0, 5.5]) + ax.set_ylim([-22, -30]) + + fig.tight_layout() + fig.savefig(os.path.join(path_ex, 'Mi_z.pdf'), dpi=300) + + # Emission line loop + for j, line in enumerate(line_calc_names): + + # Summary figures + fig, axs = plt.subplots(1, 2, figsize=(12,5)) + + x = np.linspace(1000, 12000) + axs[0].plot(x, x, color='gray') + + x = np.linspace(41, 48) + axs[1].plot(x, x, color='gray', zorder=-1) + + axs[0].scatter(line_fwhm_all[:, j], line_fwhms[:, j], color='r', marker='o', alpha=0.5) + rmse_fwhm = rmse(line_fwhm_all[:, j], line_fwhms[:, j]) + print(f'RMSE FWHM = {rmse_fwhm}') + axs[0].set_xlim([1000, 12000]) + axs[0].set_ylim([1000, 12000]) + + axs[1].scatter(line_L_all[:, j], line_Ls[:, j], color='r', marker='o', alpha=0.5) + rmse_L = rmse(line_fwhm_all[:, j], line_fwhms[:, j]) + print(f'RMSE L = {rmse_L}') + axs[1].set_xlim([41, 46]) + axs[1].set_ylim([41, 46]) + + axs[0].set_title(line) + axs[0].set_xlabel(f'FWHM v{pyqsofit.__version__}', fontsize=20) + axs[0].set_ylabel(f'FWHM Shen 2011', fontsize=20) + + axs[1].set_title(line) + axs[1].set_xlabel(f'log L v{pyqsofit.__version__}', fontsize=20) + axs[1].set_ylabel(f'log L Shen 2011', fontsize=20) + + fig.tight_layout() + fig.savefig(os.path.join(path_ex, f'{line}.pdf'), dpi=300) + + # Test + #assert rmse_L < 0.2 + + end = timeit.default_timer() + print('finshed in '+str(round(end-start))+'s') + + return + +# init +import sys +if __name__ == "__main__": + a = int(sys.argv[1]) + test_dr7(a) \ No newline at end of file