From 3e5d232e3684edce25e4fd59519c0928cada6ddc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Boulogne?= Date: Wed, 11 Jun 2025 08:36:35 +0200 Subject: [PATCH] init doc --- check.py | 97 +- docs/docs/Makefile | 20 + docs/docs/_build/.buildinfo | 4 + .../_build/.doctrees/api_reference.doctree | Bin 0 -> 2681 bytes docs/docs/_build/.doctrees/environment.pickle | Bin 0 -> 19566 bytes docs/docs/_build/.doctrees/example.doctree | Bin 0 -> 4141 bytes docs/docs/_build/.doctrees/examples.doctree | Bin 0 -> 4142 bytes docs/docs/_build/.doctrees/index.doctree | Bin 0 -> 5115 bytes .../_build/.doctrees/installation.doctree | Bin 0 -> 4759 bytes .../_build/_sources/api_reference.rst.txt | 10 + docs/docs/_build/_sources/example.rst.txt | 34 + docs/docs/_build/_sources/examples.rst.txt | 34 + docs/docs/_build/_sources/index.rst.txt | 24 + .../docs/_build/_sources/installation.rst.txt | 28 + docs/docs/_build/_static/alabaster.css | 663 +++++++++++++ docs/docs/_build/_static/basic.css | 906 ++++++++++++++++++ docs/docs/_build/_static/custom.css | 1 + docs/docs/_build/_static/doctools.js | 149 +++ .../_build/_static/documentation_options.js | 13 + docs/docs/_build/_static/file.png | Bin 0 -> 286 bytes docs/docs/_build/_static/github-banner.svg | 5 + docs/docs/_build/_static/language_data.js | 192 ++++ docs/docs/_build/_static/minus.png | Bin 0 -> 90 bytes docs/docs/_build/_static/plus.png | Bin 0 -> 90 bytes docs/docs/_build/_static/pygments.css | 84 ++ docs/docs/_build/_static/searchtools.js | 635 ++++++++++++ docs/docs/_build/_static/sphinx_highlight.js | 154 +++ docs/docs/_build/api_reference.html | 111 +++ docs/docs/_build/example.html | 133 +++ docs/docs/_build/examples.html | 140 +++ docs/docs/_build/genindex.html | 105 ++ docs/docs/_build/index.html | 135 +++ docs/docs/_build/installation.html | 134 +++ docs/docs/_build/objects.inv | Bin 0 -> 293 bytes docs/docs/_build/search.html | 123 +++ docs/docs/_build/searchindex.js | 1 + docs/docs/api_reference.rst | 10 + docs/docs/conf.py | 40 + docs/docs/examples.rst | 34 + docs/docs/index.rst | 24 + docs/docs/installation.rst | 28 + docs/docs/make.bat | 35 + optifik/analysis.py | 5 +- optifik/fft.py | 2 +- optifik/minmax.py | 4 + optifik/scheludko.py | 114 ++- tests/test_SV1.py | 12 - tests/test_SV2o0.py | 15 +- tests/test_SV2o1.py | 13 +- tests/test_basic.py | 28 +- 50 files changed, 4194 insertions(+), 105 deletions(-) create mode 100644 docs/docs/Makefile create mode 100644 docs/docs/_build/.buildinfo create mode 100644 docs/docs/_build/.doctrees/api_reference.doctree create mode 100644 docs/docs/_build/.doctrees/environment.pickle create mode 100644 docs/docs/_build/.doctrees/example.doctree create mode 100644 docs/docs/_build/.doctrees/examples.doctree create mode 100644 docs/docs/_build/.doctrees/index.doctree create mode 100644 docs/docs/_build/.doctrees/installation.doctree create mode 100644 docs/docs/_build/_sources/api_reference.rst.txt create mode 100644 docs/docs/_build/_sources/example.rst.txt create mode 100644 docs/docs/_build/_sources/examples.rst.txt create mode 100644 docs/docs/_build/_sources/index.rst.txt create mode 100644 docs/docs/_build/_sources/installation.rst.txt create mode 100644 docs/docs/_build/_static/alabaster.css create mode 100644 docs/docs/_build/_static/basic.css create mode 100644 docs/docs/_build/_static/custom.css create mode 100644 docs/docs/_build/_static/doctools.js create mode 100644 docs/docs/_build/_static/documentation_options.js create mode 100644 docs/docs/_build/_static/file.png create mode 100644 docs/docs/_build/_static/github-banner.svg create mode 100644 docs/docs/_build/_static/language_data.js create mode 100644 docs/docs/_build/_static/minus.png create mode 100644 docs/docs/_build/_static/plus.png create mode 100644 docs/docs/_build/_static/pygments.css create mode 100644 docs/docs/_build/_static/searchtools.js create mode 100644 docs/docs/_build/_static/sphinx_highlight.js create mode 100644 docs/docs/_build/api_reference.html create mode 100644 docs/docs/_build/example.html create mode 100644 docs/docs/_build/examples.html create mode 100644 docs/docs/_build/genindex.html create mode 100644 docs/docs/_build/index.html create mode 100644 docs/docs/_build/installation.html create mode 100644 docs/docs/_build/objects.inv create mode 100644 docs/docs/_build/search.html create mode 100644 docs/docs/_build/searchindex.js create mode 100644 docs/docs/api_reference.rst create mode 100644 docs/docs/conf.py create mode 100644 docs/docs/examples.rst create mode 100644 docs/docs/index.rst create mode 100644 docs/docs/installation.rst create mode 100644 docs/docs/make.bat diff --git a/check.py b/check.py index ef6afa8..9ac554b 100644 --- a/check.py +++ b/check.py @@ -7,8 +7,6 @@ import matplotlib.pyplot as plt from optifik.analysis import * -from optifik.fft import Prominence_from_fft -from optifik.auto import auto from optifik import io plt.rc('text', usetex=True) @@ -20,9 +18,45 @@ plt.rcParams.update({ }) - -def play(): +def play_oder1(): ##### Chemin du dossier contenant le spectre ##### + from optifik.scheludko import thickness_from_scheludko + + DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic')) + + #SAVE_FOLDER = DATA_FOLDER + + # FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51 + # FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35 + # FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ² + # FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2 + # FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2 + + FILE_NAME = '000004310.xy' #TEST# + spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME) + + + + lambdas, intensities = io.load_spectrum(spectrum_file) + plot_spectrum(lambdas, intensities, title='Raw') + + lambdas, intensities = io.load_spectrum(spectrum_file, lambda_min=450) + plot_spectrum(lambdas, intensities, title='Raw, cropped') + + smoothed_intensities = smooth_intensities(intensities) + plot_spectrum(lambdas, smoothed_intensities, title='Smoothed') + + refractive_index = 1.324188 + 3102.060378 / (lambdas**2) + prominence = 0.025 + peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities, + min_peak_prominence=prominence, + plot=True) + + + +def play_order1(): + ##### Chemin du dossier contenant le spectre ##### + from optifik.scheludko import thickness_from_scheludko DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic')) @@ -38,7 +72,7 @@ def play(): spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME) - spectrum_file = 'tests/spectraVictor1/T5469.xy' #TEST# + spectrum_file = 'tests/spectraVictor2/order1/T10219.xy' #TEST# lambdas, intensities = io.load_spectrum(spectrum_file) plot_spectrum(lambdas, intensities, title='Raw') @@ -49,19 +83,59 @@ def play(): smoothed_intensities = smooth_intensities(intensities) plot_spectrum(lambdas, smoothed_intensities, title='Smoothed') - prominence = 0.02 + refractive_index = 1.324188 + 3102.060378 / (lambdas**2) + prominence = 0.025 peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities, min_peak_prominence=prominence, plot=True) - indice = 1.324188 + 3102.060378 / (lambdas**2) - p, s, w = Prominence_from_fft(lambdas, smoothed_intensities, indice, plot=True) + result = thickness_from_scheludko(lambdas, smoothed_intensities, + refractive_index=refractive_index, + min_peak_prominence=prominence, + plot=True) - print(p) +def play_order0(): + ##### Chemin du dossier contenant le spectre ##### + from optifik.scheludko import thickness_for_order0 + + DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic')) + + #SAVE_FOLDER = DATA_FOLDER + + # FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51 + # FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35 + # FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ² + # FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2 + # FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2 + + FILE_NAME = '000004310.xy' #TEST# + spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME) + + + spectrum_file = 'tests/spectraVictor2/order0/T14787.xy' #TEST# + + lambdas, intensities = io.load_spectrum(spectrum_file) + plot_spectrum(lambdas, intensities, title='Raw') + + lambdas, intensities = io.load_spectrum(spectrum_file, lambda_min=450) + plot_spectrum(lambdas, intensities, title='Raw, cropped') + + smoothed_intensities = smooth_intensities(intensities) + plot_spectrum(lambdas, smoothed_intensities, title='Smoothed') + + refractive_index = 1.324188 + 3102.060378 / (lambdas**2) + prominence = .02 peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities, - min_peak_prominence=p, + min_peak_prominence=prominence, plot=True) + result = thickness_for_order0(lambdas, smoothed_intensities, + refractive_index=refractive_index, + min_peak_prominence=prominence, + plot=True) + + + def check_basic(): ##### Chemin du dossier contenant le spectre ##### @@ -139,4 +213,5 @@ if __name__ == '__main__': #check_basic() #check_SV1() - play() + #play() + play_order0() diff --git a/docs/docs/Makefile b/docs/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/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/docs/_build/.buildinfo b/docs/docs/_build/.buildinfo new file mode 100644 index 0000000..80d809d --- /dev/null +++ b/docs/docs/_build/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. 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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; 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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; +} + +/* -- 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/docs/_build/_static/custom.css b/docs/docs/_build/_static/custom.css new file mode 100644 index 0000000..2a924f1 --- /dev/null +++ b/docs/docs/_build/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/docs/docs/_build/_static/doctools.js b/docs/docs/_build/_static/doctools.js new file mode 100644 index 0000000..0398ebb --- /dev/null +++ b/docs/docs/_build/_static/doctools.js @@ -0,0 +1,149 @@ +/* + * Base JavaScript utilities for all Sphinx HTML documentation. + */ +"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/docs/_build/_static/documentation_options.js b/docs/docs/_build/_static/documentation_options.js new file mode 100644 index 0000000..7e4c114 --- /dev/null +++ b/docs/docs/_build/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '', + 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/docs/_build/_static/file.png b/docs/docs/_build/_static/file.png new file mode 100644 index 0000000000000000000000000000000000000000..a858a410e4faa62ce324d814e4b816fff83a6fb3 GIT binary patch literal 286 zcmV+(0pb3MP)s`hMrGg#P~ix$^RISR_I47Y|r1 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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/docs/_build/_static/minus.png b/docs/docs/_build/_static/minus.png new file mode 100644 index 0000000000000000000000000000000000000000..d96755fdaf8bb2214971e0db9c1fd3077d7c419d GIT binary patch literal 90 zcmeAS@N?(olHy`uVBq!ia0vp^+#t*WBp7;*Yy1LIik>cxAr*|t7R?Mi>2?kWtu=nj kDsEF_5m^0CR;1wuP-*O&G^0G}KYk!hp00i_>zopr08q^qX#fBK literal 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a/docs/docs/_build/_static/searchtools.js b/docs/docs/_build/_static/searchtools.js new file mode 100644 index 0000000..91f4be5 --- /dev/null +++ b/docs/docs/_build/_static/searchtools.js @@ -0,0 +1,635 @@ +/* + * Sphinx JavaScript utilities for the full-text search. + */ +"use strict"; + +/** + * 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, kind] = 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, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +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, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + 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 = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${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, kind]. +// 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 [".headerlink", "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.setAttribute("role", "list"); + 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, kind]. + 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) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // 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], + SearchResultKind.index, + ]; + 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]], + SearchResultKind.object, + ]); + }; + 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 = []; + // find documents, if any, containing the query word in their text/title term indices + // use Object.hasOwnProperty to avoid mismatching against prototype properties + const arr = [ + { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term }, + { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, 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, new Map()); + const fileScores = scoreMap.get(file); + fileScores.set(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).get(w))); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + 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/docs/_build/_static/sphinx_highlight.js b/docs/docs/_build/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/docs/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( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * 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/docs/_build/api_reference.html b/docs/docs/_build/api_reference.html new file mode 100644 index 0000000..0eb4964 --- /dev/null +++ b/docs/docs/_build/api_reference.html @@ -0,0 +1,111 @@ + + + + + + + + API Reference — optifik documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

API Reference

+

Below is the complete reference for Optifik’s public API.

+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/example.html b/docs/docs/_build/example.html new file mode 100644 index 0000000..3761579 --- /dev/null +++ b/docs/docs/_build/example.html @@ -0,0 +1,133 @@ + + + + + + + + Examples — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Examples

+
+

Basic Optimization

+

Here’s a simple example using Optifik to solve a quadratic function.

+
from optifik import minimize
+
+def quadratic(x):
+    return (x - 3) ** 2
+
+result = minimize(quadratic, x0=0)
+print(result)
+
+
+
+
+

Constrained Optimization

+
from optifik import minimize
+
+def objective(x):
+    return x[0] ** 2 + x[1] ** 2
+
+def constraint(x):
+    return x[0] + x[1] - 1
+
+result = minimize(objective, x0=[0, 0], constraints=[constraint])
+print(result)
+
+
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/examples.html b/docs/docs/_build/examples.html new file mode 100644 index 0000000..ca5effb --- /dev/null +++ b/docs/docs/_build/examples.html @@ -0,0 +1,140 @@ + + + + + + + + Examples — optifik documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Examples

+
+

Basic Optimization

+

Here’s a simple example using Optifik to solve a quadratic function.

+
from optifik import minimize
+
+def quadratic(x):
+    return (x - 3) ** 2
+
+result = minimize(quadratic, x0=0)
+print(result)
+
+
+
+
+

Constrained Optimization

+
from optifik import minimize
+
+def objective(x):
+    return x[0] ** 2 + x[1] ** 2
+
+def constraint(x):
+    return x[0] + x[1] - 1
+
+result = minimize(objective, x0=[0, 0], constraints=[constraint])
+print(result)
+
+
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/genindex.html b/docs/docs/_build/genindex.html new file mode 100644 index 0000000..dfd33e8 --- /dev/null +++ b/docs/docs/_build/genindex.html @@ -0,0 +1,105 @@ + + + + + + + Index — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ +
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/index.html b/docs/docs/_build/index.html new file mode 100644 index 0000000..ddf8987 --- /dev/null +++ b/docs/docs/_build/index.html @@ -0,0 +1,135 @@ + + + + + + + + Optifik Documentation — optifik documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Optifik Documentation

+

Welcome to the documentation for Optifik, a Python library for

+
+

Contents

+
+

Documentation

+ +
+
+
+

Indices and tables

+ +
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/installation.html b/docs/docs/_build/installation.html new file mode 100644 index 0000000..592a514 --- /dev/null +++ b/docs/docs/_build/installation.html @@ -0,0 +1,134 @@ + + + + + + + + Installation — optifik documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Installation

+

You can install Optifik using pip:

+
pip install optifik
+
+
+

Alternatively, you can install it from source:

+
git clone https://github.com/yourusername/optifik.git
+cd optifik
+pip install -e .
+
+
+
+

Requirements

+
    +

  • Python >= 3.8

    • +

  • NumPy >= 1.21

    • +
+

Optional for extended functionality:

+
    +

  • SciPy

    • +

  • Matplotlib

    • +
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/objects.inv b/docs/docs/_build/objects.inv new file mode 100644 index 0000000000000000000000000000000000000000..3425d3fd71c1080b61cc19f65e73dfa6a28d5787 GIT binary patch literal 293 zcmY#Z2rkIT%&Sny%qvUHE6FdaR47X=D$dN$Q!wIERtPA{&q_@$u~Nt{D9KFA%mxaD zL8Pq|fb5WrRE46{+{Dbhl++@H{4|A90J?O%6T%lOnzC-weTW|5ah~b%l$}GdMjgttA^BUZ>vZj-F?h!)fgI&*EgitJb38 o;!W3g$W7l`za?u)nN@l^dyC(eYQwaPmB;oqvE3Apy*=>&000zvZ~y=R literal 0 HcmV?d00001 diff --git a/docs/docs/_build/search.html b/docs/docs/_build/search.html new file mode 100644 index 0000000..70179d7 --- /dev/null +++ b/docs/docs/_build/search.html @@ -0,0 +1,123 @@ + + + + + + + Search — optifik documentation + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Search

+ + + + +

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

+ + +
+ + + +
+ + +
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/docs/_build/searchindex.js b/docs/docs/_build/searchindex.js new file mode 100644 index 0000000..b151b37 --- /dev/null +++ b/docs/docs/_build/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles":{"API Reference":[[0,null]],"Basic Optimization":[[1,"basic-optimization"]],"Constrained Optimization":[[1,"constrained-optimization"]],"Contents":[[2,"contents"]],"Documentation":[[2,null]],"Examples":[[1,null]],"Indices and tables":[[2,"indices-and-tables"]],"Installation":[[3,null]],"Optifik Documentation":[[2,null]],"Requirements":[[3,"requirements"]]},"docnames":["api_reference","examples","index","installation"],"envversion":{"sphinx":65,"sphinx.domains.c":3,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":9,"sphinx.domains.index":1,"sphinx.domains.javascript":3,"sphinx.domains.math":2,"sphinx.domains.python":4,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.viewcode":1},"filenames":["api_reference.rst","examples.rst","index.rst","installation.rst"],"indexentries":{},"objects":{},"objnames":{},"objtypes":{},"terms":{"":[0,1],"0":1,"1":[1,3],"2":1,"21":3,"3":[1,3],"8":3,"altern":3,"api":2,"basic":2,"below":0,"can":3,"cd":3,"clone":3,"com":3,"complet":0,"constrain":2,"constraint":1,"def":1,"e":3,"exampl":2,"extend":3,"from":[1,3],"function":[1,3],"git":3,"github":3,"here":1,"http":3,"i":0,"import":1,"index":2,"instal":2,"librari":2,"matplotlib":3,"minim":1,"modul":2,"numpi":3,"object":1,"optifik":[0,1,3],"optim":2,"option":3,"page":2,"pip":3,"print":1,"public":0,"python":[2,3],"quadrat":1,"refer":2,"requir":2,"result":1,"return":1,"scipi":3,"search":2,"simpl":1,"solv":1,"sourc":3,"us":[1,3],"welcom":2,"x":1,"x0":1,"you":3,"yourusernam":3},"titles":["API Reference","Examples","Optifik Documentation","Installation"],"titleterms":{"api":0,"basic":1,"constrain":1,"content":2,"document":2,"exampl":1,"indic":2,"instal":3,"optifik":2,"optim":1,"refer":0,"requir":3,"tabl":2}}) \ No newline at end of file diff --git a/docs/docs/api_reference.rst b/docs/docs/api_reference.rst new file mode 100644 index 0000000..62b478b --- /dev/null +++ b/docs/docs/api_reference.rst @@ -0,0 +1,10 @@ +API Reference +============= + +Below is the complete reference for Optifik's public API. + +.. automodule:: optifik.core + :members: + :undoc-members: + :show-inheritance: + diff --git a/docs/docs/conf.py b/docs/docs/conf.py new file mode 100644 index 0000000..3985532 --- /dev/null +++ b/docs/docs/conf.py @@ -0,0 +1,40 @@ +import os +import sys +sys.path.insert(0, os.path.abspath('../optifik')) + +# 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 + +project = 'optifik' +copyright = '2025, F. Boulogne et al.' +author = 'F. Boulogne et al.' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.napoleon', + 'sphinx.ext.viewcode', +] + +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'] + + +napoleon_google_docstring = False +napoleon_numpy_docstring = True + diff --git a/docs/docs/examples.rst b/docs/docs/examples.rst new file mode 100644 index 0000000..735e8c7 --- /dev/null +++ b/docs/docs/examples.rst @@ -0,0 +1,34 @@ +Examples +======== + +Basic Optimization +------------------ + +Here's a simple example using Optifik to solve a quadratic function. + +.. code-block:: python + + from optifik import minimize + + def quadratic(x): + return (x - 3) ** 2 + + result = minimize(quadratic, x0=0) + print(result) + +Constrained Optimization +------------------------ + +.. code-block:: python + + from optifik import minimize + + def objective(x): + return x[0] ** 2 + x[1] ** 2 + + def constraint(x): + return x[0] + x[1] - 1 + + result = minimize(objective, x0=[0, 0], constraints=[constraint]) + print(result) + diff --git a/docs/docs/index.rst b/docs/docs/index.rst new file mode 100644 index 0000000..d9ef27d --- /dev/null +++ b/docs/docs/index.rst @@ -0,0 +1,24 @@ +Optifik Documentation +===================== + +Welcome to the documentation for **Optifik**, a Python library for + + +Contents +-------- + +.. toctree:: + :maxdepth: 2 + :caption: Documentation + + installation + api_reference + examples + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/docs/docs/installation.rst b/docs/docs/installation.rst new file mode 100644 index 0000000..a0e132e --- /dev/null +++ b/docs/docs/installation.rst @@ -0,0 +1,28 @@ +Installation +============ + +You can install Optifik using `pip`: + +.. code-block:: bash + + pip install optifik + +Alternatively, you can install it from source: + +.. code-block:: bash + + git clone https://github.com/yourusername/optifik.git + cd optifik + pip install -e . + +Requirements +------------ + +- Python >= 3.8 +- NumPy >= 1.21 + +Optional for extended functionality: + +- SciPy +- Matplotlib + diff --git a/docs/docs/make.bat b/docs/docs/make.bat new file mode 100644 index 0000000..32bb245 --- /dev/null +++ b/docs/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/optifik/analysis.py b/optifik/analysis.py index 35ff5fb..addddc3 100644 --- a/optifik/analysis.py +++ b/optifik/analysis.py @@ -46,8 +46,6 @@ def finds_peak(wavelengths, intensities, min_peak_prominence, min_peak_distance= (peaks_min, peaks_max) """ - - peaks_max, _ = find_peaks(intensities, prominence=min_peak_prominence, distance=min_peak_distance) peaks_min, _ = find_peaks(-intensities, prominence=min_peak_prominence, distance=min_peak_distance) @@ -59,10 +57,11 @@ def finds_peak(wavelengths, intensities, min_peak_prominence, min_peak_distance= plt.xlabel(r'$\lambda$ (nm)') plt.ylabel(r'$I^*$') plt.legend() + import inspect + plt.title(inspect.currentframe().f_code.co_name) plt.tight_layout() plt.show() - return peaks_min, peaks_max diff --git a/optifik/fft.py b/optifik/fft.py index 5a81290..b1cdec9 100644 --- a/optifik/fft.py +++ b/optifik/fft.py @@ -74,7 +74,7 @@ def thickness_from_fft(wavelengths, intensities, thickness_fft = freq_max / 2. if plot: - plt.figure(figsize=(10, 6),dpi =600) + plt.figure(figsize=(10, 6), dpi=300) plt.loglog(inverse_wavelengths_fft, np.abs(intensities_fft)) plt.loglog(freq_max, np.abs(intensities_fft[idx_max_fft]), 'o') plt.xlabel('Frequency') diff --git a/optifik/minmax.py b/optifik/minmax.py index 4085332..52be9de 100644 --- a/optifik/minmax.py +++ b/optifik/minmax.py @@ -116,6 +116,8 @@ def thickness_from_minmax(wavelengths, ax.legend() ax.set_title(f'Thickness = {thickness_minmax:.2f} nm') + import inspect + plt.title(inspect.currentframe().f_code.co_name) plt.tight_layout() plt.show() @@ -140,6 +142,8 @@ def thickness_from_minmax(wavelengths, ax.legend() ax.set_title(f'Thickness = {thickness_minmax:.2f} nm') + import inspect + plt.title(inspect.currentframe().f_code.co_name) plt.tight_layout() plt.show() diff --git a/optifik/scheludko.py b/optifik/scheludko.py index 369c0c3..10f64f4 100644 --- a/optifik/scheludko.py +++ b/optifik/scheludko.py @@ -165,7 +165,17 @@ def thickness_from_scheludko(wavelengths, peaks_min, peaks_max = finds_peak(wavelengths, intensities, min_peak_prominence=min_peak_prominence, - plot=False) + plot=plot) + + failure, message = False, '' + if len(peaks_min) == 0: + message += 'Failed to detect at least one minimum. ' + failure = True + if len(peaks_max) == 0: + message += 'Failed to detect at least one maximum. ' + failure = True + if failure: + raise RuntimeError(message) # Get the last oscillation peaks lambda_min = wavelengths[peaks_min[-1]] @@ -181,9 +191,9 @@ def thickness_from_scheludko(wavelengths, r_index_masked = r_index[mask] intensities_masked = intensities[mask] - min_ecart = np.inf + min_difference = np.inf best_m = None - best_h = None + best_h_values = None if plot: plt.figure(figsize=(10, 6), dpi=300) @@ -195,19 +205,21 @@ def thickness_from_scheludko(wavelengths, intensities_masked, m, r_index_masked) - ecart = np.max(h_values) - np.min(h_values) + difference = np.max(h_values) - np.min(h_values) - print(f"Écart pour m={m} : {ecart:.3f} nm") + print(f"h-difference for m={m}: {difference:.1f} nm") - if ecart < min_ecart: - min_ecart = ecart + if difference < min_difference: + min_difference = difference best_m = m - best_h = h_values + best_h_values = h_values if plot: plt.plot(wavelengths_masked, h_values,'.', markersize=3, label=f"Épaisseur du film (Scheludko, m={m})") + print(f"Optimized: m={best_m}") + # Delta num = intensities_masked - np.min(intensities_masked) denom = np.max(intensities_masked) - np.min(intensities_masked) @@ -217,14 +229,15 @@ def thickness_from_scheludko(wavelengths, # DeltaVrai = (intensities_raw_masked -np.min(intensities_raw_masked))/(np.max(intensities_raw_masked) -np.min(intensities_raw_masked)) DeltaScheludko = Delta(wavelengths_masked, - np.mean(best_h), + np.mean(best_h_values), best_m, r_index_masked) xdata = (wavelengths_masked, r_index_masked) - popt, pcov = curve_fit(lambda x, h: Delta_fit(x, h, m), xdata, DeltaVrai, p0=[np.mean(best_h)]) + popt, pcov = curve_fit(lambda x, h: Delta_fit(x, h, m), xdata, DeltaVrai, p0=[np.mean(best_h_values)]) fitted_h = popt[0] + std_err = np.sqrt(pcov[0][0]) if plot: Delta_values = Delta(wavelengths_masked, fitted_h, best_m, r_index_masked) @@ -232,15 +245,22 @@ def thickness_from_scheludko(wavelengths, plt.figure(figsize=(10, 6), dpi=300) plt.plot(wavelengths_masked, DeltaVrai, 'bo-', markersize=2, label=r'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$') + + # Scheludko + label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(best_h_values):.1f} \pm {np.std(best_h_values):.1f}\ \mathrm{{nm}})$' plt.plot(wavelengths_masked, DeltaScheludko, - 'go-', markersize=2, label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(best_h):.1f} \pm {np.std(best_h):.1f}\ \mathrm{{nm}})$') - plt.plot(wavelengths_masked, Delta_values, 'ro-',markersize=2, label=rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {np.sqrt(pcov[0][0]):.1f} \ \mathrm{{nm}})$') + 'go-', markersize=2, label=label) + # Fit + label = rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {std_err:.1f} \ \mathrm{{nm}})$' + plt.plot(wavelengths_masked, Delta_values, 'ro-', markersize=2, label=label) + plt.legend() plt.ylabel(r'$\Delta$') plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)') + import inspect + plt.title(inspect.currentframe().f_code.co_name) - - return OptimizeResult(thickness=fitted_h,) + return OptimizeResult(thickness=fitted_h, stderr=std_err) def thickness_for_order0(wavelengths, @@ -258,9 +278,11 @@ def thickness_for_order0(wavelengths, peaks_min, peaks_max = finds_peak(wavelengths, intensities, min_peak_prominence=min_peak_prominence, - plot=False) + plot=plot) + if len(peaks_max) != 1: + raise RuntimeError('Failed to detect a single maximum peak.') lambda_unique = wavelengths[peaks_max[0]] @@ -272,50 +294,54 @@ def thickness_for_order0(wavelengths, intensities_masked = intensities[mask] intensities_I_min_masked =intensities_I_min[mask] - # best_m = None - # best_h = None - - - m = 0 - h_values = thickness_scheludko_at_order(wavelengths_masked, - intensities_masked, - 0, - r_index_masked, - Imin=intensities_I_min_masked) + # We assume to be at order zero. + best_m = 0 + best_h_values = thickness_scheludko_at_order(wavelengths_masked, + intensities_masked, + best_m, + r_index_masked, + Imin=intensities_I_min_masked) if plot: plt.figure(figsize=(10, 6), dpi=300) - plt.plot(wavelengths_masked, h_values, label=r"Épaisseur du film (Scheludko, m=0)") - - - best_m = m - best_h = h_values + plt.plot(wavelengths_masked, best_h_values, label=r"Épaisseur du film (Scheludko, m=0)") + plt.ylabel(r'$h$ ($\mathrm{{nm}}$)') + plt.xlabel(r'$\lambda$ (nm)') + import inspect + plt.title(inspect.currentframe().f_code.co_name) # Delta num = intensities_masked - np.min(intensities_I_min_masked) denom = np.max(intensities_masked) - np.min(intensities_I_min_masked) DeltaVrai = num / denom - DeltaScheludko = Delta(wavelengths_masked, np.mean(best_h), best_m, r_index_masked) - #print(np.mean(best_h),np.std(best_h)) - - if plot: - plt.figure(figsize=(10, 6), dpi=300) - plt.plot(wavelengths_masked,DeltaVrai,'bo-', markersize=2,label=r'$\mathrm{{Raw}}\ \mathrm{{Data}}$') - plt.plot(wavelengths_masked,DeltaScheludko,'ro-', markersize=2,label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(best_h):.1f} \pm {np.std(best_h):.1f}\ \mathrm{{nm}})$') - + DeltaScheludko = Delta(wavelengths_masked, np.mean(best_h_values), best_m, r_index_masked) + #print(np.mean(best_h_values),np.std(best_h_values)) xdata = (wavelengths_masked, r_index_masked) - popt, pcov = curve_fit(lambda x, h: Delta_fit(x, h, m), xdata, DeltaVrai, p0=[np.mean(best_h)]) + popt, pcov = curve_fit(lambda x, h: Delta_fit(x, h, best_m), xdata, DeltaVrai, p0=[np.mean(best_h_values)]) fitted_h = popt[0] + std_err = np.sqrt(pcov[0][0]) if plot: Delta_values = Delta(wavelengths_masked, fitted_h, best_m, r_index_masked) - plt.plot(wavelengths_masked, Delta_values, - 'go-', markersize=2, - label=rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {np.sqrt(pcov[0][0]):.1f} \ \mathrm{{nm}})$') + + plt.figure(figsize=(10, 6), dpi=300) + plt.plot(wavelengths_masked, DeltaVrai, + 'bo-', markersize=2, label=r'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$') + + # Scheludko + label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(best_h_values):.1f} \pm {np.std(best_h_values):.1f}\ \mathrm{{nm}})$' + plt.plot(wavelengths_masked, DeltaScheludko, + 'go-', markersize=2, label=label) + # Fit + label = rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {std_err:.1f} \ \mathrm{{nm}})$' + plt.plot(wavelengths_masked, Delta_values, 'ro-', markersize=2, label=label) + plt.legend() plt.ylabel(r'$\Delta$') - plt.xlabel(r'$\lambda$ (nm)') + plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)') + import inspect + plt.title(inspect.currentframe().f_code.co_name) - return OptimizeResult(thickness=fitted_h,) + return OptimizeResult(thickness=fitted_h, stderr=std_err) diff --git a/tests/test_SV1.py b/tests/test_SV1.py index 88be384..8129a4f 100644 --- a/tests/test_SV1.py +++ b/tests/test_SV1.py @@ -7,7 +7,6 @@ from optifik.minmax import thickness_from_minmax from optifik.io import load_spectrum from optifik.analysis import smooth_intensities from optifik.analysis import finds_peak -from optifik.fft import Prominence_from_fft import yaml @@ -32,22 +31,11 @@ def test_minmax(spectrum_path, expected): indice = 1.324188 + 3102.060378 / (lambdas**2) prominence = 0.02 - #prominence, s, w = Prominence_from_fft(lambdas, smoothed_intensities, indice) - #prominence *= 10 - thickness_minmax = thickness_from_minmax(lambdas, smoothed_intensities, refractive_index=indice, min_peak_prominence=prominence) - #prominence, s, w = Prominence_from_fft(lambdas, smoothed_intensities, indice) - #print(f'Prom: {prominence}') - #indice = 1.324188 + 3102.060378 / (w**2) - #thickness_minmax = thickness_from_minmax(w, - # s, - # refractive_index=indice, - # min_peak_prominence=prominence) - result = thickness_minmax.thickness assert_allclose(result, expected, rtol=1e-1) diff --git a/tests/test_SV2o0.py b/tests/test_SV2o0.py index f686797..ef90093 100644 --- a/tests/test_SV2o0.py +++ b/tests/test_SV2o0.py @@ -20,21 +20,20 @@ def load(): return data -@pytest.mark.skip('...') +#@pytest.mark.skip('...') @pytest.mark.parametrize("spectrum_path, expected", load()) def test_SV2o0(spectrum_path, expected): lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450) smoothed_intensities = smooth_intensities(raw_intensities) refractive_index = 1.324188 + 3102.060378 / (lambdas**2) - prominence = 0.02 + prominence = 0.020 - thickness_scheludko = thickness_for_order0(lambdas, smoothed_intensities, - refractive_index=refractive_index, - min_peak_prominence=prominence, - plot=False) - result = thickness_scheludko.thickness + result = thickness_for_order0(lambdas, smoothed_intensities, + refractive_index=refractive_index, + min_peak_prominence=prominence, + plot=False) - assert_allclose(result, expected, rtol=1e-1) + assert_allclose(result.thickness, expected, rtol=1e-1) diff --git a/tests/test_SV2o1.py b/tests/test_SV2o1.py index ed6f096..843df27 100644 --- a/tests/test_SV2o1.py +++ b/tests/test_SV2o1.py @@ -28,14 +28,13 @@ def test_SV2o1(spectrum_path, expected): smoothed_intensities = smooth_intensities(raw_intensities) refractive_index = 1.324188 + 3102.060378 / (lambdas**2) - prominence = 0.02 + prominence = 0.020 - thickness_scheludko = thickness_from_scheludko(lambdas, smoothed_intensities, - refractive_index=refractive_index, - min_peak_prominence=prominence, - plot=False) - result = thickness_scheludko.thickness + result = thickness_from_scheludko(lambdas, smoothed_intensities, + refractive_index=refractive_index, + min_peak_prominence=prominence, + plot=False) - assert_allclose(result, expected, rtol=1e-1) + assert_allclose(result.thickness, expected, rtol=1e-1) diff --git a/tests/test_basic.py b/tests/test_basic.py index 3038c3a..35b0b06 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -8,7 +8,6 @@ from optifik.minmax import thickness_from_minmax from optifik.scheludko import thickness_from_scheludko from optifik.scheludko import thickness_for_order0 from optifik.analysis import smooth_intensities -from optifik.fft import Prominence_from_fft from optifik.io import load_spectrum @@ -39,21 +38,16 @@ def test_minmax_ransac(): smoothed_intensities = smooth_intensities(raw_intensities) indice = 1.324188 + 3102.060378 / (lambdas**2) - prominence, signal, wavelength = Prominence_from_fft(lambdas, - smoothed_intensities, - refractive_index=indice, - plot=False) + prominence = 0.02 + result = thickness_from_minmax(lambdas, + smoothed_intensities, + refractive_index=indice, + min_peak_prominence=prominence, + method='ransac', + plot=False) - thickness_minmax = thickness_from_minmax(lambdas, - smoothed_intensities, - refractive_index=indice, - min_peak_prominence=prominence, - method='ransac', - plot=False) - result = thickness_minmax.thickness - - assert_allclose(result, expected, rtol=1e-1) + assert_allclose(result.thickness, expected, rtol=1e-1) def test_scheludko_4peaks(): @@ -66,11 +60,7 @@ def test_scheludko_4peaks(): smoothed_intensities = smooth_intensities(raw_intensities) indice = 1.324188 + 3102.060378 / (lambdas**2) - prominence, signal, wavelength = Prominence_from_fft(lambdas, - smoothed_intensities, - refractive_index=indice, - plot=False) - + prominence = 0.02 result = thickness_from_scheludko(lambdas, smoothed_intensities, refractive_index=indice,