From da61334f40da41206a00f32121dc357ff039bd8a Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Tue, 10 Oct 2023 13:22:00 +0000 Subject: [PATCH] build based on 9005db5 --- previews/PR276/.documenter-siteinfo.json | 1 + .../PR276/advanced/custom_branch/index.html | 30 + .../PR276/advanced/reduce_latency/index.html | 26 + previews/PR276/assets/documenter.js | 874 ++++++++++++++++++ .../PR276/assets/themes/documenter-dark.css | 7 + .../PR276/assets/themes/documenter-light.css | 9 + previews/PR276/assets/themeswap.js | 84 ++ previews/PR276/assets/unroot.png | Bin 0 -> 15106 bytes previews/PR276/assets/unroot.svg | 173 ++++ previews/PR276/assets/warner.js | 52 ++ previews/PR276/devdocs/index.html | 2 + previews/PR276/exampleusage/index.html | 32 + previews/PR276/index.html | 87 ++ previews/PR276/internalapis/index.html | 126 +++ previews/PR276/performancetips/index.html | 9 + previews/PR276/search_index.js | 3 + previews/PR276/siteinfo.js | 1 + 17 files changed, 1516 insertions(+) create mode 100644 previews/PR276/.documenter-siteinfo.json create mode 100644 previews/PR276/advanced/custom_branch/index.html create mode 100644 previews/PR276/advanced/reduce_latency/index.html create mode 100644 previews/PR276/assets/documenter.js create mode 100644 previews/PR276/assets/themes/documenter-dark.css create mode 100644 previews/PR276/assets/themes/documenter-light.css create mode 100644 previews/PR276/assets/themeswap.js create mode 100644 previews/PR276/assets/unroot.png create mode 100644 previews/PR276/assets/unroot.svg create mode 100644 previews/PR276/assets/warner.js create mode 100644 previews/PR276/devdocs/index.html create mode 100644 previews/PR276/exampleusage/index.html create mode 100644 previews/PR276/index.html create mode 100644 previews/PR276/internalapis/index.html create mode 100644 previews/PR276/performancetips/index.html create mode 100644 previews/PR276/search_index.js create mode 100644 previews/PR276/siteinfo.js diff --git a/previews/PR276/.documenter-siteinfo.json b/previews/PR276/.documenter-siteinfo.json new file mode 100644 index 00000000..9bb4422e --- /dev/null +++ b/previews/PR276/.documenter-siteinfo.json @@ -0,0 +1 @@ +{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-10T13:21:55","documenter_version":"1.1.0"}} \ No newline at end of file diff --git a/previews/PR276/advanced/custom_branch/index.html b/previews/PR276/advanced/custom_branch/index.html new file mode 100644 index 00000000..686f69cf --- /dev/null +++ b/previews/PR276/advanced/custom_branch/index.html @@ -0,0 +1,30 @@ + +Parse Custom Branch · UnROOT.jl

Parse Custom Branch

It is possible to parse Branches with custom structure as long as you know how the bytes should be interpreted. As an example, the TLorentzVector is added using this mechanism and we will walk through the steps needed:

1. Provide a map between fClassName of your struct (as seen in .root) to a Julia type.

Pass a Dict{String, Type} to ROOTFile(filepath; customstructs). The TLorentzVector is shipped by default:

ROOTFile(filepath; customstructs = Dict("TLorentzVector" => LorentzVector{Float64}))

This Dict will subsequently be used by the auto_T_JaggT function at here such that when we encounter a branch with this fClassName, we will return your Type as the detected element type of this branch.

2. Extend the raw bytes interpreting function UnROOT.interped_data

By default, given a branch element type and a "jaggness" type, a general function is defined which will try to parse the raw bytes into Julia data structure. The ::Type{T} will match what you have provided in the Dict in the previous step.

Thus, to "teach" UnROOT how to interpret bytes for your type T, you would want to defined a more specific UnROOT.interped_data than the default one. Taking the TLorentzVector as example again, we define a function:

using LorentzVector
+const LVF64 = LorentzVector{Float64}
+function UnROOT.interped_data(rawdata, rawoffsets, ::Type{LVF64}, ::Type{J}) where {T, J <: JaggType}
+    # `rawoffsets` is actually redundant, since we know each TLV is always 64 bytes (withe 32 bytes header)
+    [
+     reinterpret(LVF64, x) for x in Base.Iterators.partition(rawdata, 64)
+    ]
+end
+
+# VorView is defined in the `src/custom.jl`
+function Base.reinterpret(::Type{LVF64}, v::VorView) where T
+    # x,y,z,t in ROOT
+    v4 = ntoh.(reinterpret(Float64, v[1+32:end]))
+    # t,x,y,z in LorentzVectors.jl
+    LVF64(v4[4], v4[1], v4[2], v4[3])
+end

The Base.reinterpret function is just a helper function, you could instead write everything inside UnROOT.interped_data. We then builds on these, to interpret Jagged TLV branch: https://github.com/JuliaHEP/UnROOT.jl/blob/4747f6f5fd97ed1a872765485b4eb9e99ec5a650/src/custom.jl#L47

More details

To expand a bit what we're doing here, the rawdata for a single TLV is always 64 bytes long and the first 32 bytes are TObject header which we don't care (which is why we don't care about rawoffsets here). The last 32 bytes make up 4 Float64 and we simply parse them and return a collection of (julia) LorentzVector{Float64}.

In general, if auto_T_JaggT returned MyType as promised branch element type, then

UnROOT.interped_data(rawdata, rawoffsets, ::Type{MyType},

should return Vector{MyType} because UnROOT.interped_data receives raw bytes of a basket at a time.

And that's it! Afterwards both LazyBranch and LazyTree will be able to constructed with correct type and also knows how to interpret bytes when you indexing or iterating through them

Reading Raw Data from Branch

Alternatively, reading raw data is also possible using the UnROOT.array(f::ROOTFile, path; raw=true) method. The output can be then reinterpreted using a custom type with the method UnROOT.splitup(data, offsets, T::Type; skipbytes=0, jagged=true). This provides more fine grain control in case your branch is highly irregular. You can then define suitable Julia type and readtype method for parsing these data. Alternatively, you can of course parse the data and offsets entirely manually. Here is it in action, with the help of the types from custom.jl, and some data from the KM3NeT experiment:

julia> using UnROOT
+
+julia> f = ROOTFile("test/samples/km3net_online.root")
+ROOTFile("test/samples/km3net_online.root") with 10 entries and 41 streamers.
+
+julia> data, offsets = array(f, "KM3NET_EVENT/KM3NET_EVENT/snapshotHits"; raw=true)
+2058-element Array{UInt8,1}:
+ 0x00
+ 0x03
+   ⋮
+   
+julia> UnROOT.splitup(data, offsets, UnROOT._KM3NETDAQHit)
+4-element Vector{Vector{UnROOT._KM3NETDAQHit}}:
+ [UnROOT._KM3NETDAQHit(1073742790, 0x00, 9, 0x60)......
diff --git a/previews/PR276/advanced/reduce_latency/index.html b/previews/PR276/advanced/reduce_latency/index.html new file mode 100644 index 00000000..6b5aea23 --- /dev/null +++ b/previews/PR276/advanced/reduce_latency/index.html @@ -0,0 +1,26 @@ + +Reduce startup latency · UnROOT.jl

Bake sysimage with PackageCompiler.jl

You can bake a sysimage tailored for your analysis to reduce latency.

> cat readtree.jl
+using UnROOT
+
+const r = ROOTFile("/home/akako/.julia/dev/UnROOT/test/samples/NanoAODv5_sample.root")
+
+const t = LazyTree(r, "Events", ["nMuon", "Electron_dxy"])
+
+
+@show t[1, :Electron_dxy]
+
+> time julia --startup-file=no readtree.jl
+t[1, :Electron_dxy] = Float32[0.00037050247]
+
+________________________________________________________
+Executed in   10.82 secs    fish           external
+   usr time   11.09 secs  580.00 micros   11.09 secs
+   sys time    0.65 secs  189.00 micros    0.65 secs

In Julia, `]add PackageCompiler':

julia> using PackageCompiler
+
+julia> PackageCompiler.create_sysimage(:UnROOT; precompile_statements_file="./readtree.jl", sysimage_path="./unroot.so", replace_default=false)'

profit:

> time julia -J ./unroot.so readtree.jl 
+t[1, :Electron_dxy] = Float32[0.00037050247]
+
+________________________________________________________
+Executed in  619.20 millis    fish           external
+   usr time  902.29 millis    0.00 millis  902.29 millis
+   sys time  658.59 millis    1.05 millis  657.54 millis
diff --git a/previews/PR276/assets/documenter.js b/previews/PR276/assets/documenter.js new file mode 100644 index 00000000..7002e251 --- /dev/null +++ b/previews/PR276/assets/documenter.js @@ -0,0 +1,874 @@ +// Generated by Documenter.jl +requirejs.config({ + paths: { + 'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/languages/julia.min', + 'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/headroom.min', + 'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.13.2/jquery-ui.min', + 'minisearch': 'https://cdn.jsdelivr.net/npm/minisearch@6.1.0/dist/umd/index.min', + 'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/contrib/auto-render.min', + 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.0/jquery.min', + 'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/jQuery.headroom.min', + 'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min', + 'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/highlight.min', + 'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.8.0/languages/julia-repl.min', + }, + shim: { + "highlight-julia": { + "deps": [ + "highlight" + ] + }, + "katex-auto-render": { + "deps": [ + "katex" + ] + }, + "headroom-jquery": { + "deps": [ + "jquery", + "headroom" + ] + }, + "highlight-julia-repl": { + "deps": [ + "highlight" + ] + } +} +}); +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) { +$(document).ready(function() { + renderMathInElement( + document.body, + { + "delimiters": [ + { + "left": "$", + "right": "$", + "display": false + }, + { + "left": "$$", + "right": "$$", + "display": true + }, + { + "left": "\\[", + "right": "\\]", + "display": true + } + ] +} + + ); +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) { +$(document).ready(function() { + hljs.highlightAll(); +}) + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +var isExpanded = true; + +$(document).on("click", ".docstring header", function () { + let articleToggleTitle = "Expand docstring"; + + if ($(this).siblings("section").is(":visible")) { + $(this) + .find(".docstring-article-toggle-button") + .removeClass("fa-chevron-down") + .addClass("fa-chevron-right"); + } else { + $(this) + .find(".docstring-article-toggle-button") + .removeClass("fa-chevron-right") + .addClass("fa-chevron-down"); + + articleToggleTitle = "Collapse docstring"; + } + + $(this) + .find(".docstring-article-toggle-button") + .prop("title", articleToggleTitle); + $(this).siblings("section").slideToggle(); +}); + +$(document).on("click", ".docs-article-toggle-button", function () { + let articleToggleTitle = "Expand docstring"; + let navArticleToggleTitle = "Expand all docstrings"; + + if (isExpanded) { + $(this).removeClass("fa-chevron-up").addClass("fa-chevron-down"); + $(".docstring-article-toggle-button") + .removeClass("fa-chevron-down") + .addClass("fa-chevron-right"); + + isExpanded = false; + + $(".docstring section").slideUp(); + } else { + $(this).removeClass("fa-chevron-down").addClass("fa-chevron-up"); + $(".docstring-article-toggle-button") + .removeClass("fa-chevron-right") + .addClass("fa-chevron-down"); + + isExpanded = true; + articleToggleTitle = "Collapse docstring"; + navArticleToggleTitle = "Collapse all docstrings"; + + $(".docstring section").slideDown(); + } + + $(this).prop("title", navArticleToggleTitle); + $(".docstring-article-toggle-button").prop("title", articleToggleTitle); +}); + +}) +//////////////////////////////////////////////////////////////////////////////// +require([], function() { +function addCopyButtonCallbacks() { + for (const el of document.getElementsByTagName("pre")) { + const button = document.createElement("button"); + button.classList.add("copy-button", "fa-solid", "fa-copy"); + button.setAttribute("aria-label", "Copy this code block"); + button.setAttribute("title", "Copy"); + + el.appendChild(button); + + const success = function () { + button.classList.add("success", "fa-check"); + button.classList.remove("fa-copy"); + }; + + const failure = function () { + button.classList.add("error", "fa-xmark"); + button.classList.remove("fa-copy"); + }; + + button.addEventListener("click", function () { + copyToClipboard(el.innerText).then(success, failure); + + setTimeout(function () { + button.classList.add("fa-copy"); + button.classList.remove("success", "fa-check", "fa-xmark"); + }, 5000); + }); + } +} + +function copyToClipboard(text) { + // clipboard API is only available in secure contexts + if (window.navigator && window.navigator.clipboard) { + return window.navigator.clipboard.writeText(text); + } else { + return new Promise(function (resolve, reject) { + try { + const el = document.createElement("textarea"); + el.textContent = text; + el.style.position = "fixed"; + el.style.opacity = 0; + document.body.appendChild(el); + el.select(); + document.execCommand("copy"); + + resolve(); + } catch (err) { + reject(err); + } finally { + document.body.removeChild(el); + } + }); + } +} + +if (document.readyState === "loading") { + document.addEventListener("DOMContentLoaded", addCopyButtonCallbacks); +} else { + addCopyButtonCallbacks(); +} + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) { + +// Manages the top navigation bar (hides it when the user starts scrolling down on the +// mobile). +window.Headroom = Headroom; // work around buggy module loading? +$(document).ready(function () { + $("#documenter .docs-navbar").headroom({ + tolerance: { up: 10, down: 10 }, + }); +}); + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery', 'minisearch'], function($, minisearch) { + +// In general, most search related things will have "search" as a prefix. +// To get an in-depth about the thought process you can refer: https://hetarth02.hashnode.dev/series/gsoc + +let results = []; +let timer = undefined; + +let data = documenterSearchIndex["docs"].map((x, key) => { + x["id"] = key; // minisearch requires a unique for each object + return x; +}); + +// list below is the lunr 2.1.3 list minus the intersect with names(Base) +// (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with) +// ideally we'd just filter the original list but it's not available as a variable +const stopWords = new Set([ + "a", + "able", + "about", + "across", + "after", + "almost", + "also", + "am", + "among", + "an", + "and", + "are", + "as", + "at", + "be", + "because", + "been", + "but", + "by", + "can", + "cannot", + "could", + "dear", + "did", + "does", + "either", + "ever", + "every", + "from", + "got", + "had", + "has", + "have", + "he", + "her", + "hers", + "him", + "his", + "how", + "however", + "i", + "if", + "into", + "it", + "its", + "just", + "least", + "like", + "likely", + "may", + "me", + "might", + "most", + "must", + "my", + "neither", + "no", + "nor", + "not", + "of", + "off", + "often", + "on", + "or", + "other", + "our", + "own", + "rather", + "said", + "say", + "says", + "she", + "should", + "since", + "so", + "some", + "than", + "that", + "the", + "their", + "them", + "then", + "there", + "these", + "they", + "this", + "tis", + "to", + "too", + "twas", + "us", + "wants", + "was", + "we", + "were", + "what", + "when", + "who", + "whom", + "why", + "will", + "would", + "yet", + "you", + "your", +]); + +let index = new minisearch({ + fields: ["title", "text"], // fields to index for full-text search + storeFields: ["location", "title", "text", "category", "page"], // fields to return with search results + processTerm: (term) => { + let word = stopWords.has(term) ? null : term; + if (word) { + // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names + word = word + .replace(/^[^a-zA-Z0-9@!]+/, "") + .replace(/[^a-zA-Z0-9@!]+$/, ""); + } + + return word ?? null; + }, + // add . as a separator, because otherwise "title": "Documenter.Anchors.add!", would not find anything if searching for "add!", only for the entire qualification + tokenize: (string) => string.split(/[\s\-\.]+/), + // options which will be applied during the search + searchOptions: { + boost: { title: 100 }, + fuzzy: 2, + processTerm: (term) => { + let word = stopWords.has(term) ? null : term; + if (word) { + word = word + .replace(/^[^a-zA-Z0-9@!]+/, "") + .replace(/[^a-zA-Z0-9@!]+$/, ""); + } + + return word ?? null; + }, + tokenize: (string) => string.split(/[\s\-\.]+/), + }, +}); + +index.addAll(data); + +let filters = [...new Set(data.map((x) => x.category))]; +var modal_filters = make_modal_body_filters(filters); +var filter_results = []; + +$(document).on("keyup", ".documenter-search-input", function (event) { + // Adding a debounce to prevent disruptions from super-speed typing! + debounce(() => update_search(filter_results), 300); +}); + +$(document).on("click", ".search-filter", function () { + if ($(this).hasClass("search-filter-selected")) { + $(this).removeClass("search-filter-selected"); + } else { + $(this).addClass("search-filter-selected"); + } + + // Adding a debounce to prevent disruptions from crazy clicking! + debounce(() => get_filters(), 300); +}); + +/** + * A debounce function, takes a function and an optional timeout in milliseconds + * + * @function callback + * @param {number} timeout + */ +function debounce(callback, timeout = 300) { + clearTimeout(timer); + timer = setTimeout(callback, timeout); +} + +/** + * Make/Update the search component + * + * @param {string[]} selected_filters + */ +function update_search(selected_filters = []) { + let initial_search_body = ` +
Type something to get started!
+ `; + + let querystring = $(".documenter-search-input").val(); + + if (querystring.trim()) { + results = index.search(querystring, { + filter: (result) => { + // Filtering results + if (selected_filters.length === 0) { + return result.score >= 1; + } else { + return ( + result.score >= 1 && selected_filters.includes(result.category) + ); + } + }, + }); + + let search_result_container = ``; + let search_divider = `
`; + + if (results.length) { + let links = []; + let count = 0; + let search_results = ""; + + results.forEach(function (result) { + if (result.location) { + // Checking for duplication of results for the same page + if (!links.includes(result.location)) { + search_results += make_search_result(result, querystring); + count++; + } + + links.push(result.location); + } + }); + + let result_count = `
${count} result(s)
`; + + search_result_container = ` +
+ ${modal_filters} + ${search_divider} + ${result_count} +
+ ${search_results} +
+
+ `; + } else { + search_result_container = ` +
+ ${modal_filters} + ${search_divider} +
0 result(s)
+
+
No result found!
+ `; + } + + if ($(".search-modal-card-body").hasClass("is-justify-content-center")) { + $(".search-modal-card-body").removeClass("is-justify-content-center"); + } + + $(".search-modal-card-body").html(search_result_container); + } else { + filter_results = []; + modal_filters = make_modal_body_filters(filters, filter_results); + + if (!$(".search-modal-card-body").hasClass("is-justify-content-center")) { + $(".search-modal-card-body").addClass("is-justify-content-center"); + } + + $(".search-modal-card-body").html(initial_search_body); + } +} + +/** + * Make the modal filter html + * + * @param {string[]} filters + * @param {string[]} selected_filters + * @returns string + */ +function make_modal_body_filters(filters, selected_filters = []) { + let str = ``; + + filters.forEach((val) => { + if (selected_filters.includes(val)) { + str += `${val}`; + } else { + str += `${val}`; + } + }); + + let filter_html = ` +
+ Filters: + ${str} +
+ `; + + return filter_html; +} + +/** + * Make the result component given a minisearch result data object and the value of the search input as queryString. + * To view the result object structure, refer: https://lucaong.github.io/minisearch/modules/_minisearch_.html#searchresult + * + * @param {object} result + * @param {string} querystring + * @returns string + */ +function make_search_result(result, querystring) { + let search_divider = `
`; + let display_link = + result.location.slice(Math.max(0), Math.min(50, result.location.length)) + + (result.location.length > 30 ? "..." : ""); // To cut-off the link because it messes with the overflow of the whole div + + if (result.page !== "") { + display_link += ` (${result.page})`; + } + + let textindex = new RegExp(`\\b${querystring}\\b`, "i").exec(result.text); + let text = + textindex !== null + ? result.text.slice( + Math.max(textindex.index - 100, 0), + Math.min( + textindex.index + querystring.length + 100, + result.text.length + ) + ) + : ""; // cut-off text before and after from the match + + let display_result = text.length + ? "..." + + text.replace( + new RegExp(`\\b${querystring}\\b`, "i"), // For first occurrence + '$&' + ) + + "..." + : ""; // highlights the match + + let in_code = false; + if (!["page", "section"].includes(result.category.toLowerCase())) { + in_code = true; + } + + // We encode the full url to escape some special characters which can lead to broken links + let result_div = ` + +
+
${result.title}
+
${result.category}
+
+

+ ${display_result} +

+
+ ${display_link} +
+ + ${search_divider} + `; + + return result_div; +} + +/** + * Get selected filters, remake the filter html and lastly update the search modal + */ +function get_filters() { + let ele = $(".search-filters .search-filter-selected").get(); + filter_results = ele.map((x) => $(x).text().toLowerCase()); + modal_filters = make_modal_body_filters(filters, filter_results); + update_search(filter_results); +} + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// Modal settings dialog +$(document).ready(function () { + var settings = $("#documenter-settings"); + $("#documenter-settings-button").click(function () { + settings.toggleClass("is-active"); + }); + // Close the dialog if X is clicked + $("#documenter-settings button.delete").click(function () { + settings.removeClass("is-active"); + }); + // Close dialog if ESC is pressed + $(document).keyup(function (e) { + if (e.keyCode == 27) settings.removeClass("is-active"); + }); +}); + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +let search_modal_header = ` +
+
+

+ + + + +

+
+
+ +
+
+`; + +let initial_search_body = ` +
Type something to get started!
+`; + +let search_modal_footer = ` + +`; + +$(document.body).append( + ` + + ` +); + +document.querySelector(".docs-search-query").addEventListener("click", () => { + openModal(); +}); + +document.querySelector(".close-search-modal").addEventListener("click", () => { + closeModal(); +}); + +$(document).on("click", ".search-result-link", function () { + closeModal(); +}); + +document.addEventListener("keydown", (event) => { + if ((event.ctrlKey || event.metaKey) && event.key === "/") { + openModal(); + } else if (event.key === "Escape") { + closeModal(); + } + + return false; +}); + +// Functions to open and close a modal +function openModal() { + let searchModal = document.querySelector("#search-modal"); + + searchModal.classList.add("is-active"); + document.querySelector(".documenter-search-input").focus(); +} + +function closeModal() { + let searchModal = document.querySelector("#search-modal"); + let initial_search_body = ` +
Type something to get started!
+ `; + + searchModal.classList.remove("is-active"); + document.querySelector(".documenter-search-input").blur(); + + if (!$(".search-modal-card-body").hasClass("is-justify-content-center")) { + $(".search-modal-card-body").addClass("is-justify-content-center"); + } + + $(".documenter-search-input").val(""); + $(".search-modal-card-body").html(initial_search_body); +} + +document + .querySelector("#search-modal .modal-background") + .addEventListener("click", () => { + closeModal(); + }); + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// Manages the showing and hiding of the sidebar. +$(document).ready(function () { + var sidebar = $("#documenter > .docs-sidebar"); + var sidebar_button = $("#documenter-sidebar-button"); + sidebar_button.click(function (ev) { + ev.preventDefault(); + sidebar.toggleClass("visible"); + if (sidebar.hasClass("visible")) { + // Makes sure that the current menu item is visible in the sidebar. + $("#documenter .docs-menu a.is-active").focus(); + } + }); + $("#documenter > .docs-main").bind("click", function (ev) { + if ($(ev.target).is(sidebar_button)) { + return; + } + if (sidebar.hasClass("visible")) { + sidebar.removeClass("visible"); + } + }); +}); + +// Resizes the package name / sitename in the sidebar if it is too wide. +// Inspired by: https://github.com/davatron5000/FitText.js +$(document).ready(function () { + e = $("#documenter .docs-autofit"); + function resize() { + var L = parseInt(e.css("max-width"), 10); + var L0 = e.width(); + if (L0 > L) { + var h0 = parseInt(e.css("font-size"), 10); + e.css("font-size", (L * h0) / L0); + // TODO: make sure it survives resizes? + } + } + // call once and then register events + resize(); + $(window).resize(resize); + $(window).on("orientationchange", resize); +}); + +// Scroll the navigation bar to the currently selected menu item +$(document).ready(function () { + var sidebar = $("#documenter .docs-menu").get(0); + var active = $("#documenter .docs-menu .is-active").get(0); + if (typeof active !== "undefined") { + sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15; + } +}); + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// Theme picker setup +$(document).ready(function () { + // onchange callback + $("#documenter-themepicker").change(function themepick_callback(ev) { + var themename = $("#documenter-themepicker option:selected").attr("value"); + if (themename === "auto") { + // set_theme(window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light'); + window.localStorage.removeItem("documenter-theme"); + } else { + // set_theme(themename); + window.localStorage.setItem("documenter-theme", themename); + } + // We re-use the global function from themeswap.js to actually do the swapping. + set_theme_from_local_storage(); + }); + + // Make sure that the themepicker displays the correct theme when the theme is retrieved + // from localStorage + if (typeof window.localStorage !== "undefined") { + var theme = window.localStorage.getItem("documenter-theme"); + if (theme !== null) { + $("#documenter-themepicker option").each(function (i, e) { + e.selected = e.value === theme; + }); + } + } +}); + +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { + +// update the version selector with info from the siteinfo.js and ../versions.js files +$(document).ready(function () { + // If the version selector is disabled with DOCUMENTER_VERSION_SELECTOR_DISABLED in the + // siteinfo.js file, we just return immediately and not display the version selector. + if ( + typeof DOCUMENTER_VERSION_SELECTOR_DISABLED === "boolean" && + DOCUMENTER_VERSION_SELECTOR_DISABLED + ) { + return; + } + + var version_selector = $("#documenter .docs-version-selector"); + var version_selector_select = $("#documenter .docs-version-selector select"); + + version_selector_select.change(function (x) { + target_href = version_selector_select + .children("option:selected") + .get(0).value; + window.location.href = target_href; + }); + + // add the current version to the selector based on siteinfo.js, but only if the selector is empty + if ( + typeof DOCUMENTER_CURRENT_VERSION !== "undefined" && + $("#version-selector > option").length == 0 + ) { + var option = $( + "" + ); + version_selector_select.append(option); + } + + if (typeof DOC_VERSIONS !== "undefined") { + var existing_versions = version_selector_select.children("option"); + var existing_versions_texts = existing_versions.map(function (i, x) { + return x.text; + }); + DOC_VERSIONS.forEach(function (each) { + var version_url = documenterBaseURL + "/../" + each + "/"; + var existing_id = $.inArray(each, existing_versions_texts); + // if not already in the version selector, add it as a new option, + // otherwise update the old option with the URL and enable it + if (existing_id == -1) { + var option = $( + "" + ); + version_selector_select.append(option); + } else { + var option = existing_versions[existing_id]; + option.value = version_url; + option.disabled = false; + } + }); + } + + // only show the version selector if the selector has been populated + if (version_selector_select.children("option").length > 0) { + version_selector.toggleClass("visible"); + } +}); + +}) diff --git a/previews/PR276/assets/themes/documenter-dark.css b/previews/PR276/assets/themes/documenter-dark.css new file mode 100644 index 00000000..691b83ab --- /dev/null +++ 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h1,html.theme--documenter-dark .content h2,html.theme--documenter-dark .content h3,html.theme--documenter-dark .content h4,html.theme--documenter-dark .content h5,html.theme--documenter-dark .content h6{color:#f2f2f2;font-weight:600;line-height:1.125}html.theme--documenter-dark .content h1{font-size:2em;margin-bottom:0.5em}html.theme--documenter-dark .content h1:not(:first-child){margin-top:1em}html.theme--documenter-dark .content h2{font-size:1.75em;margin-bottom:0.5714em}html.theme--documenter-dark .content h2:not(:first-child){margin-top:1.1428em}html.theme--documenter-dark .content h3{font-size:1.5em;margin-bottom:0.6666em}html.theme--documenter-dark .content h3:not(:first-child){margin-top:1.3333em}html.theme--documenter-dark .content h4{font-size:1.25em;margin-bottom:0.8em}html.theme--documenter-dark .content h5{font-size:1.125em;margin-bottom:0.8888em}html.theme--documenter-dark .content h6{font-size:1em;margin-bottom:1em}html.theme--documenter-dark .content 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.docs-logo>img.is-5by4{padding-top:80%}html.theme--documenter-dark .image.is-4by3,html.theme--documenter-dark #documenter .docs-sidebar .docs-logo>img.is-4by3{padding-top:75%}html.theme--documenter-dark .image.is-3by2,html.theme--documenter-dark #documenter .docs-sidebar .docs-logo>img.is-3by2{padding-top:66.6666%}html.theme--documenter-dark .image.is-5by3,html.theme--documenter-dark #documenter .docs-sidebar .docs-logo>img.is-5by3{padding-top:60%}html.theme--documenter-dark .image.is-16by9,html.theme--documenter-dark #documenter .docs-sidebar .docs-logo>img.is-16by9{padding-top:56.25%}html.theme--documenter-dark .image.is-2by1,html.theme--documenter-dark #documenter .docs-sidebar .docs-logo>img.is-2by1{padding-top:50%}html.theme--documenter-dark .image.is-3by1,html.theme--documenter-dark #documenter .docs-sidebar .docs-logo>img.is-3by1{padding-top:33.3333%}html.theme--documenter-dark .image.is-4by5,html.theme--documenter-dark #documenter .docs-sidebar 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+ Maintainer: @highlightjs/core-team + Website: https://highlightjs.org/ + License: see project LICENSE + Touched: 2021 +*/pre code.hljs{display:block;overflow-x:auto;padding:1em}code.hljs{padding:3px 5px}.hljs{background:#F3F3F3;color:#444}.hljs-comment{color:#697070}.hljs-tag,.hljs-punctuation{color:#444a}.hljs-tag .hljs-name,.hljs-tag .hljs-attr{color:#444}.hljs-keyword,.hljs-attribute,.hljs-selector-tag,.hljs-meta .hljs-keyword,.hljs-doctag,.hljs-name{font-weight:bold}.hljs-type,.hljs-string,.hljs-number,.hljs-selector-id,.hljs-selector-class,.hljs-quote,.hljs-template-tag,.hljs-deletion{color:#880000}.hljs-title,.hljs-section{color:#880000;font-weight:bold}.hljs-regexp,.hljs-symbol,.hljs-variable,.hljs-template-variable,.hljs-link,.hljs-selector-attr,.hljs-operator,.hljs-selector-pseudo{color:#ab5656}.hljs-literal{color:#695}.hljs-built_in,.hljs-bullet,.hljs-code,.hljs-addition{color:#397300}.hljs-meta{color:#1f7199}.hljs-meta .hljs-string{color:#38a}.hljs-emphasis{font-style:italic}.hljs-strong{font-weight:bold} diff --git a/previews/PR276/assets/themeswap.js b/previews/PR276/assets/themeswap.js new file mode 100644 index 00000000..9f5eebe6 --- /dev/null +++ b/previews/PR276/assets/themeswap.js @@ -0,0 +1,84 @@ +// Small function to quickly swap out themes. Gets put into the tag.. +function set_theme_from_local_storage() { + // Initialize the theme to null, which means default + var theme = null; + // If the browser supports the localstorage and is not disabled then try to get the + // documenter theme + if (window.localStorage != null) { + // Get the user-picked theme from localStorage. May be `null`, which means the default + // theme. + theme = window.localStorage.getItem("documenter-theme"); + } + // Check if the users preference is for dark color scheme + var darkPreference = + window.matchMedia("(prefers-color-scheme: dark)").matches === true; + // Initialize a few variables for the loop: + // + // - active: will contain the index of the theme that should be active. Note that there + // is no guarantee that localStorage contains sane values. If `active` stays `null` + // we either could not find the theme or it is the default (primary) theme anyway. + // Either way, we then need to stick to the primary theme. + // + // - disabled: style sheets that should be disabled (i.e. all the theme style sheets + // that are not the currently active theme) + var active = null; + var disabled = []; + var primaryLightTheme = null; + var primaryDarkTheme = null; + for (var i = 0; i < document.styleSheets.length; i++) { + var ss = document.styleSheets[i]; + // The tag of each style sheet is expected to have a data-theme-name attribute + // which must contain the name of the theme. The names in localStorage much match this. + var themename = ss.ownerNode.getAttribute("data-theme-name"); + // attribute not set => non-theme stylesheet => ignore + if (themename === null) continue; + // To distinguish the default (primary) theme, it needs to have the data-theme-primary + // attribute set. + if (ss.ownerNode.getAttribute("data-theme-primary") !== null) { + primaryLightTheme = themename; + } + // Check if the theme is primary dark theme so that we could store its name in darkTheme + if (ss.ownerNode.getAttribute("data-theme-primary-dark") !== null) { + primaryDarkTheme = themename; + } + // If we find a matching theme (and it's not the default), we'll set active to non-null + if (themename === theme) active = i; + // Store the style sheets of inactive themes so that we could disable them + if (themename !== theme) disabled.push(ss); + } + var activeTheme = null; + if (active !== null) { + // If we did find an active theme, we'll (1) add the theme--$(theme) class to + document.getElementsByTagName("html")[0].className = "theme--" + theme; + activeTheme = theme; + } else { + // If we did _not_ find an active theme, then we need to fall back to the primary theme + // which can either be dark or light, depending on the user's OS preference. + var activeTheme = darkPreference ? primaryDarkTheme : primaryLightTheme; + // In case it somehow happens that the relevant primary theme was not found in the + // preceding loop, we abort without doing anything. + if (activeTheme === null) { + console.error("Unable to determine primary theme."); + return; + } + // When switching to the primary light theme, then we must not have a class name + // for the tag. That's only for non-primary or the primary dark theme. + if (darkPreference) { + document.getElementsByTagName("html")[0].className = + "theme--" + activeTheme; + } else { + document.getElementsByTagName("html")[0].className = ""; + } + } + for (var i = 0; i < document.styleSheets.length; i++) { + var ss = document.styleSheets[i]; + // The tag of each style sheet is expected to have a data-theme-name attribute + // which must contain the name of the theme. The names in localStorage much match this. + var themename = ss.ownerNode.getAttribute("data-theme-name"); + // attribute not set => non-theme stylesheet => ignore + if (themename === null) continue; + // we'll disable all the stylesheets, except for the active one + ss.disabled = !(themename == activeTheme); + } +} +set_theme_from_local_storage(); diff --git a/previews/PR276/assets/unroot.png b/previews/PR276/assets/unroot.png new file mode 100644 index 0000000000000000000000000000000000000000..bd4a468b239a4f6f0f2909954d9915e41b8f6b05 GIT binary patch literal 15106 zcmX9_1z1z>+diW~TDn6}N@8@!1Qh9#AJQ)!>2WEt2LDLw`RtXat_$4L$HLtP@bU3^YUk|WVP)ZJ^VG%NHe+9!4ggqy=P(65 z-^{%%A76&C)AM#)IEQhHV9Iy%sRAWMhPN;AIg)^g-}uOnfMANZ!AEvHtRHdlVi`Cg zShz7xdvnQ7EJ-Z(cpRfZm6FKdiD`_@yM)r1x@PFc?aHtI(y^rGXI*~+vTd0iZ1-my zo9AWx4;nWD;$jg92my5D;%McI3WM9v<2dQRs!i=ZP>SIze*kie3)Kyd`~KmLFdexf z8uM_bAAH;~4QX)*kSZnlO1BwGGqu;Z_be%Ud7ZvwyF%T1!h&OMo;;*Mva0e@NkyaX 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zJ^409&;0jQVj28ctN$veT~-GqmhPUBV1V5r|8I3QL=N3F2{uNB>vGG8d5~$x!~)S7dv4w}nX_&MAlnHh(-m!WBWLa@j~+xt{_lZcm}4TNl*;rGPct{Fu=oC z%0syvZi(>)=nx*X1>1`_K*4SxlNwuO492naa7CTihnvcLqST}l?Z z?kZNEGJ+gxb!+RKzQ02F8{zc&&N3c@^4C*Z?~kxg_(DP^Yp19>)U3K=qEbqfq>hg@ zuD3M0&J01Vz8xqs*$4eOKYa=7gf)c3@?iv$i6hsqRZC!90XT)}xuV(}9dWIz(o-O} zpd*V~v?NtUuiAiKWga2%6JHj9$W)5(7;H6}R==2sWN?Or;JL04tB*)~C}7~o-80LZ XS^tXGJ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/previews/PR276/assets/warner.js b/previews/PR276/assets/warner.js new file mode 100644 index 00000000..3f6f5d00 --- /dev/null +++ b/previews/PR276/assets/warner.js @@ -0,0 +1,52 @@ +function maybeAddWarning() { + // DOCUMENTER_NEWEST is defined in versions.js, DOCUMENTER_CURRENT_VERSION and DOCUMENTER_STABLE + // in siteinfo.js. + // If either of these are undefined something went horribly wrong, so we abort. + if ( + window.DOCUMENTER_NEWEST === undefined || + window.DOCUMENTER_CURRENT_VERSION === undefined || + window.DOCUMENTER_STABLE === undefined + ) { + return; + } + + // Current version is not a version number, so we can't tell if it's the newest version. Abort. + if (!/v(\d+\.)*\d+/.test(window.DOCUMENTER_CURRENT_VERSION)) { + return; + } + + // Current version is newest version, so no need to add a warning. + if (window.DOCUMENTER_NEWEST === window.DOCUMENTER_CURRENT_VERSION) { + return; + } + + // Add a noindex meta tag (unless one exists) so that search engines don't index this version of the docs. + if (document.body.querySelector('meta[name="robots"]') === null) { + const meta = document.createElement("meta"); + meta.name = "robots"; + meta.content = "noindex"; + + document.getElementsByTagName("head")[0].appendChild(meta); + } + + const div = document.createElement("div"); + div.classList.add("outdated-warning-overlay"); + const closer = document.createElement("button"); + closer.classList.add("outdated-warning-closer", "delete"); + closer.addEventListener("click", function () { + document.body.removeChild(div); + }); + const href = window.documenterBaseURL + "/../" + window.DOCUMENTER_STABLE; + div.innerHTML = + 'This documentation is not for the latest stable release, but for either the development version or an older release.
Click here to go to the documentation for the latest stable release.'; + div.appendChild(closer); + document.body.appendChild(div); +} + +if (document.readyState === "loading") { + document.addEventListener("DOMContentLoaded", maybeAddWarning); +} else { + maybeAddWarning(); +} diff --git a/previews/PR276/devdocs/index.html b/previews/PR276/devdocs/index.html new file mode 100644 index 00000000..d108d4f2 --- /dev/null +++ b/previews/PR276/devdocs/index.html @@ -0,0 +1,2 @@ + +For Contributors · UnROOT.jl

While the ROOT documentation does not contain a detailed description of the binary structure, the format can be triangulated by other packages like

Here's a detailed from-scratch walk through on reading a jagged branch from a ROOT file, recommended for first time contributors or those who just want to learn about ROOT file format.

Three's also a discussion reagarding the ROOT binary format documentation on uproot's issue page.

diff --git a/previews/PR276/exampleusage/index.html b/previews/PR276/exampleusage/index.html new file mode 100644 index 00000000..5a8ecea6 --- /dev/null +++ b/previews/PR276/exampleusage/index.html @@ -0,0 +1,32 @@ + +Example Usage · UnROOT.jl

Chunk Iteration

t = LazyTree(...)
+res = 0.0
+for rang in Iterators.partition(1:lastindex(t), 10^6)
+    res += sum(t[rang].nMuon) #
+end
+res

Note, t[rang] is eager, if you don't need all branches, it's much better to use t.nMuon[rang], or limit which branches are selected during LazyTree() creation time.

This pattern works the best over network, for local files, stick with:

for evt in t
+    ...
+end

usually is the best approach.

Writting out .root files

Currently UnROOT.jl is focused on reading only, however, it's semi-trivial to leverage Python world for write operation since it's not performance critical.

You have the following choice:

Checkout configuration docs for PythonCall.jl

Most importantly, you probably want to set:

ENV["JULIA_PYTHONCALL_EXE"] = readchomp(`which python`)

before the using PythonCall line. Especially if you're using LCG or Athena or CMSSW environment.

Write out a TTree

julia> using PythonCall
+
+julia> const up = pyimport("uproot")
+
+julia> pywith(up.recreate("./example.root")) do file
+           file["mytree"] = Dict("branch1"=>1:1000, "branch2"=>rand(1000))
+       end
+
+# read it back with UnROOT.jl
+julia> using UnROOT
+
+julia> LazyTree("./example.root", "mytree")
+ Row │ branch1  branch2              
+     │ Int64    Float64              
+─────┼───────────────────────────────
+ 1   │ 1        0.5775868298287866
+ 2   │ 2        0.7245212475492369
+ 3   │ 3        0.009249240901789912
+ 4   │ 4        0.9010206670973542
+ 5   │ 5        0.7609879879740359
+ 6   │ 6        0.00916447384387542
+ 7   │ 7        0.5636229077934333
+ 8   │ 8        0.32617388561103156
+  ⋮  │    ⋮              ⋮

Write out a histogram

A histogram is just a tuple of (bincontent, binedges), see FHist.jl docs for details.

diff --git a/previews/PR276/index.html b/previews/PR276/index.html new file mode 100644 index 00000000..e92329aa --- /dev/null +++ b/previews/PR276/index.html @@ -0,0 +1,87 @@ + +Introduction · UnROOT.jl

Introduction

Apart from the pursue of performance, we also strive to provide intuitive and compostable interface. After all, "theoretically" fast doesn't mean the performance is accessible for the first-time physics user.

Status

We support reading all scalar and jagged branches of "basic" types, provide indexing and iteration interface with a "per branch" basket-cache. There is a low level API to provide interpretation functionalities for custom types and classes. As a metric, UnROOT can read all branches (~1800) of CMS NanoAOD including jagged TLorentzVector branch.

Loops aren't slow

One good thing about Julia is you can always fallback to writing loops since they are not intrinsically slower (than C/C++), certainly much faster than Python. Continuing the example from README:

julia> using UnROOT
+
+julia> f = ROOTFile("test/samples/NanoAODv5_sample.root")
+
+julia> mytree = LazyTree(f, "Events", ["Electron_dxy", "nMuon", r"Muon_(pt|eta)$"])

There are essentially two loops you can use:

julia> for event in mytree
+           ...
+       end
+
+julia> for (i, event) in enumerate(mytree)
+           # i will be index of `mytree`: 1, 2, 3...
+           ...
+       end

Both of which are compostable with @threads for multi-threading:

julia> Threads.@threads for event in mytree
+           ...
+       end
+
+julia> Threads.@threads for (i, event) in enumerate(mytree)
+           ...
+       end

Only one basket per branch will be cached so you don't have to worry about running out of RAM. At the same time, event inside the for-loop is not materialized until a field is accessed.

Laziness in Indexing, Slicing, and Looping

Laziness (or eagerness) in UnROOT generally refers to if an "event" has read each branches of the tree or not. As canonical example of eager event, consider indexing:

julia> const r = LazyTree(ROOTFile("./Run2012BC_DoubleMuParked_Muons.root"), "Events", ["nMuon", "Muon_phi"]);
+
+julia> names(r)
+2-element Vector{String}:
+ "Muon_phi"
+ "nMuon"
+
+julia> r[1]
+(Muon_phi = Float32[-0.034272723, 2.5426154], nMuon = 0x00000002)

Where the iterate() over tree is lazy:

julia> const r = LazyTree(ROOTFile("./Run2012BC_DoubleMuParked_Muons.root"), "Events", ["nMuon", "Muon_phi"]);
+
+julia> for (i, evt) in enumerate(r)
+           @show i, evt
+           break
+       end
+(i, evt) = (1, "LazyEvent with: (:tree, :idx)")

And the reading of actual data is delayed until evt.nMuon or evt.Muon_phi happens. Which means you should be careful about: Don't-"double-access".

The laziness of the main interfaces are summarized below:

mytreeenumerate(mytree)
for X in ...💤💤
@threads for X in ...💤💤
getindex(tree, row::Int)💤N/A
getindex(tree, row::Range)🚨N/A

Lazy tree construction

As seen in the previous section, LazyTrees are cheap and offer a convenient way to create an object that isolates the branches of interest. It's fairly common that multiple branches are present with slightly differring names, like pos.x, pos.y etc. The LazyTree function also takes regular expressions, as seen in the example below where r"Evt/trks/trks.pos.[xyz]" is passed, that will match the corresponding branches:

julia> f = UnROOT.samplefile("km3net_offline.root")
+ROOTFile with 2 entries and 25 streamers.
+/Users/tamasgal/Dev/UnROOT.jl/test/samples/km3net_offline.root
+├─ E (TTree)
+│  └─ "Evt"
+└─ Header (Head)
+
+julia> t = LazyTree(f, "E", ["Evt/trks/trks.id", r"Evt/trks/trks.pos.[xyz]"])
+ Row │ Evt_trks_trks_i   Evt_trks_trks_p  Evt_trks_trks_p  Evt_trks_trks_p      ⋯
+     │ SubArray{Int32,   SubArray{Float6  SubArray{Float6  SubArray{Float6      ⋯
+─────┼───────────────────────────────────────────────────────────────────────────
+ 1   │ [1, 2, 3, 4, 5,   [615.0, 615.0,   [446.0, 446.0,   [125.0, 125.0, 70.7, ⋯
+ 2   │ [1, 2, 3, 4, 5,   [533.0, 533.0,   [465.0, 465.0,   [80.7, 80.7, 39.1, 3 ⋯
+ 3   │ [1, 2, 3, 4, 5,   [593.0, 593.0,   [457.0, 457.0,   [194.0, 194.0, 96.5, ⋯
+ 4   │ [1, 2, 3, 4, 5,   [590.0, 590.0,   [440.0, 440.0,   [204.0, 204.0, 124.0 ⋯
+ 5   │ [1, 2, 3, 4, 5,   [546.0, 546.0,   [440.0, 440.0,   [58.6, 58.6, 30.1, 3 ⋯
+ 6   │ [1, 2, 3, 4, 5,   [585.0, 585.0,   [424.0, 424.0,   [202.0, 202.0, 183.0 ⋯
+ 7   │ [1, 2, 3, 4, 5,   [533.0, 533.0,   [440.0, 440.0,   [47.3, 47.3, 30.1, 2 ⋯
+ 8   │ [1, 2, 3, 4, 5,   [569.0, 569.0,   [469.0, 469.0,   [200.0, 200.0, 179.0 ⋯
+ 9   │ [1, 2, 3, 4, 5,   [557.0, 557.0,   [412.0, 412.0,   [209.0, 209.0, 101.0 ⋯
+ 10  │ [1, 2, 3, 4, 5,   [532.0, 532.0,   [443.0, 443.0,   [172.0, 172.0, 126.0 ⋯
+                                                                  1 column omitted
+
+julia> names(t)
+4-element Vector{String}:
+ "Evt_trks_trks_id"
+ "Evt_trks_trks_pos_y"
+ "Evt_trks_trks_pos_x"
+ "Evt_trks_trks_pos_z"
+
+julia> t.Evt_trks_trks_pos_y
+10-element LazyBranch{SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true},
+UnROOT.Nooffsetjagg, ArraysOfArrays.VectorOfVectors{Float64, Vector{Float64}, Vector{Int32},
+Vector{Tuple{}}}}:
+ [615.1089636184813, 615.1089636184813, … 574.836340445788, 576.5382993955498]
+ ...
+ ...

Branch names are normalised so that they contain valid characters for identifiers. The branchname Evt/trks/trks.pos.y for example is therefore converted to Evt_trks_trks_posy, which might be a bit inconvenient to use. LazyTree can rename branches based on regular expressions and subsitution strings (in Julia these are created with s"") which can be passed as Pairs. The example below shows how to use this:

julia> t = LazyTree(f, "E", [r"Evt/trks/trks.(dir|pos).([xyz])" => s"\1_\2"])
+ Row │ pos_z                dir_z                pos_y                dir_y               ⋯
+     │ SubArray{Float6      SubArray{Float6      SubArray{Float6      SubArray{Float6     ⋯
+─────┼─────────────────────────────────────────────────────────────────────────────────────
+ 1   │ [125.0, 125.0, 70.7  [-0.873, -0.873, -0  [615.0, 615.0, 585.  [-0.487, -0.487, -0 ⋯
+ 2   │ [80.7, 80.7, 39.1,   [-0.835, -0.835, -0  [533.0, 533.0, 559.  [0.521, 0.521, 0.52 ⋯
+ 3   │ [194.0, 194.0, 96.5  [-0.989, -0.989, -0  [593.0, 593.0, 581.  [-0.122, -0.122, -0 ⋯
+ 4   │ [204.0, 204.0, 124.  [-0.968, -0.968, -0  [590.0, 590.0, 571.  [-0.23, -0.23, -0.2 ⋯
+ 5   │ [58.6, 58.6, 30.1,   [-0.821, -0.821, -0  [546.0, 546.0, 565.  [0.54, 0.54, 0.54,  ⋯
+                                                                   2 columns omitted
+
+julia> names(t)
+6-element Vector{String}:
+ "pos_z"
+ "dir_z"
+ "pos_y"
+ "dir_y"
+ "dir_x"
+ "pos_x"
diff --git a/previews/PR276/internalapis/index.html b/previews/PR276/internalapis/index.html new file mode 100644 index 00000000..be690324 --- /dev/null +++ b/previews/PR276/internalapis/index.html @@ -0,0 +1,126 @@ + +APIs · UnROOT.jl

Commonly used

UnROOT.LazyBranch — Type
LazyBranch(f::ROOTFile, branch)

Construct an accessor for a given branch such that BA[idx] and or BA[1:20] is type-stable. And memory footprint is a single basket (<1MB usually). You can also iterate or map over it. If you want a concrete Vector, simply collect() the LazyBranch.

Example

julia> rf = ROOTFile("./test/samples/tree_with_large_array.root");
+
+julia> b = rf["t1/int32_array"];
+
+julia> ab = UnROOT.LazyBranch(rf, b);
+
+julia> for entry in ab
+           @show entry
+           break
+       end
+entry = 0
+
+julia> ab[begin:end]
+0
+1
+...
source
UnROOT.LazyTree — Method
LazyTree(f::ROOTFile, s::AbstractString, branche::Union{AbstractString, Regex})
+LazyTree(f::ROOTFile, s::AbstractString, branches::Vector{Union{AbstractString, Regex}})

Constructor for LazyTree, which is close to an DataFrame (interface wise), and a lazy Table (speed wise). Looping over a LazyTree is fast and type stable. Internally, LazyTree contains a typed table whose branch are LazyBranch. This means that at any given time only N baskets are cached, where N is the number of branches.

Note

Accessing with [start:stop] will return a LazyTree with concrete internal table.

Warning

Split branches are re-named, and the exact renaming may change. See Issue 156 for context.

Example

julia> mytree = LazyTree(f, "Events", ["Electron_dxy", "nMuon", r"Muon_(pt|eta)$"])
+ Row │ Electron_dxy     nMuon   Muon_eta         Muon_pt
+     │ Vector{Float32}  UInt32  Vector{Float32}  Vector{Float32}
+─────┼───────────────────────────────────────────────────────────
+ 1   │ [0.000371]       0       []               []
+ 2   │ [-0.00982]       2       [0.53, 0.229]    [19.9, 15.3]
+ 3   │ []               0       []               []
+ 4   │ [-0.00157]       0       []               []
+ ⋮   │     ⋮            ⋮             ⋮                ⋮
source
UnROOT.LazyTree — Method
function LazyTree(f::ROOTFile, tree::TTree, treepath, branches)

Creates a lazy tree object of the selected branches only. branches is vector of String, Regex or Pair{Regex, SubstitutionString}, where the first item is the regex selector and the second item the rename pattern.

source

More Internal

UnROOT.Cursor — Type

The Cursor type is embeded into Branches of a TTree such that when we need to read the content of a Branch, we don't need to go through the Directory and find the TKey and then seek to where the Branch is.

Note

The io inside a Cursor is in fact only a buffer, it is NOT a io that refers to the whole file's stream.

source
UnROOT.LeafField — Type
struct LeafField{T}
+    content_col_idx::Int
+    type::Int
+    nbits::Int
+end

Base case of field nesting, this links to a column in the RNTuple by 0-based index. T is the eltype of this field which mostly uses Julia native types except for Switch.

The type field is the RNTuple spec type number, used to record split encoding.

source
UnROOT.OffsetBuffer — Type
OffsetBuffer

Works with seek, position of the original file. Think of it as a view of IOStream that can be indexed with original positions.

source
UnROOT.Preamble — Method

Reads the preamble of an object.

The cursor will be put into the right place depending on the data.

source
UnROOT.RNTuple — Type
RNTuple

This is the struct for holding all metadata (schema) needed to completely describe and RNTuple from ROOT, just like TTree, to obtain a table-like data object, you need to use LazyTree explicitly:

Example

julia> f = ROOTFile("./test/samples/RNTuple/test_ntuple_stl_containers.root");
+
+julia> f["ntuple"]
+UnROOT.RNTuple:
+  header:
+    name: "ntuple"
+    ntuple_description: ""
+    writer_identifier: "ROOT v6.29/01"
+    schema:
+      RNTupleSchema with 13 top fields
+      ├─ :lorentz_vector ⇒ Struct
+      ├─ :vector_tuple_int32_string ⇒ Vector
+      ├─ :string ⇒ String
+      ├─ :vector_string ⇒ Vector
+...
+..
+.
+
+julia> LazyTree(f, "ntuple")
+ Row │ string  vector_int32     array_float      vector_vector_i     vector_string       vector_vector_s     variant_int32_s  vector_variant_     ⋯
+     │ String  Vector{Int32}    StaticArraysCor  Vector{Vector{I     Vector{String}      Vector{Vector{S     Union{Int32, St  Vector{Union{In     ⋯
+─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+ 1   │ one     [1]              [1.0, 1.0, 1.0]  Vector{Int32}[Int3  ["one"]             [["one"]]           1                Union{Int64, Strin  ⋯
+ 2   │ two     [1, 2]           [2.0, 2.0, 2.0]  Vector{Int32}[Int3  ["one", "two"]      [["one"], ["two"]]  two              Union{Int64, Strin  ⋯
+ 3   │ three   [1, 2, 3]        [3.0, 3.0, 3.0]  Vector{Int32}[Int3  ["one", "two", "th  [["one"], ["two"],  three            Union{Int64, Strin  ⋯
+ 4   │ four    [1, 2, 3, 4]     [4.0, 4.0, 4.0]  Vector{Int32}[Int3  ["one", "two", "th  [["one"], ["two"],  4                Union{Int64, Strin  ⋯
+ 5   │ five    [1, 2, 3, 4, 5]  [5.0, 5.0, 5.0]  Vector{Int32}[Int3  ["one", "two", "th  [["one"], ["two"],  5                Union{Int64, Strin  ⋯
+                                                                                                                                  5 columns omitted
source
UnROOT.RNTupleCardinality — Type
struct RNTupleCardinality{T}
+    content_col_idx::Int
+    nbits::Int
+end

Special field. The cardinality is basically a counter, but the data column is a leaf column of Index32 or Index64. To get a number from Cardinality, one needs to compute ary[i] - ary[i-1].

source
UnROOT.RNTupleField — Type
mutable struct RNTupleField{R, F, O, E} <: AbstractVector{E}

Not a counterpart of RNTuple field in ROOT. This is a user-facing Julia-only construct like LazyBranch that is meant to act like a lazy AbstractVector backed with file IO source and a schema field from RNTuple.schema.

  • R is the type of parent RNTuple
  • F is the type of the field in the schema
  • 'O' is the type of output when you read a cluster-worth of data
  • 'E' is the element type of O (i.e. what you get for each event (row) in iteration)
source
UnROOT.RNTupleSchema — Type
struct RNTupleSchema

A wrapper struct for print_tree implementation of the schema display.

Example

julia> f = ROOTFile("./test/samples/RNTuple/test_ntuple_stl_containers.root");
+
+julia> f["ntuple"].schema
+RNTupleSchema with 13 top fields
+├─ :lorentz_vector ⇒ Struct
+│                    ├─ :pt ⇒ Leaf{Float32}(col=26)
+│                    ├─ :eta ⇒ Leaf{Float32}(col=27)
+│                    ├─ :phi ⇒ Leaf{Float32}(col=28)
+│                    └─ :mass ⇒ Leaf{Float32}(col=29)
+├─ :vector_tuple_int32_string ⇒ Vector
+│                               ├─ :offset ⇒ Leaf{Int32}(col=9)
+│                               └─ :content ⇒ Struct
+│                                             ├─ :_1 ⇒ String
+│                                             │        ├─ :offset ⇒ Leaf{Int32}(col=37)
+│                                             │        └─ :content ⇒ Leaf{Char}(col=38)
+│                                             └─ :_0 ⇒ Leaf{Int32}(col=36)
+├─ :string ⇒ String
+│            ├─ :offset ⇒ Leaf{Int32}(col=1)
+│            └─ :content ⇒ Leaf{Char}(col=2)
+├─ :vector_string ⇒ Vector
+│                   ├─ :offset ⇒ Leaf{Int32}(col=5)
+│                   └─ :content ⇒ String
+│                                 ├─ :offset ⇒ Leaf{Int32}(col=13)
+│                                 └─ :content ⇒ Leaf{Char}(col=14)
+...
+..
+.
source
UnROOT.ROOTFile — Method
ROOTFile(filename::AbstractString; customstructs = Dict("TLorentzVector" => LorentzVector{Float64}))

ROOTFile's constructor from a file. The customstructs dictionary can be used to pass user-defined struct as value and its corresponding fClassName (in Branch) as key such that UnROOT will know to intepret them, see interped_data.

See also: LazyTree, LazyBranch

Example

julia> f = ROOTFile("test/samples/NanoAODv5_sample.root")
+ROOTFile with 2 entries and 21 streamers.
+test/samples/NanoAODv5_sample.root
+└─ Events
+   ├─ "run"
+   ├─ "luminosityBlock"
+   ├─ "event"
+   ├─ "HTXS_Higgs_pt"
+   ├─ "HTXS_Higgs_y"
+   └─ "⋮"
source
UnROOT.StdArrayField — Type
StdArrayField<N, T>

Special base-case field for a leaf field representing std::array<T, N>. This is because RNTuple would serialize it as a leaf field but with flags == 0x0001 in the field description. In total, there are two field descriptions associlated with array<>, one for meta-data (the N), the other one for the actual data.

source
UnROOT.StringField — Type
StringField

Special base-case field for String leaf field. This is because RNTuple splits a leaf String field into two columns (instead of split in field records). So we need an offset column and a content column (that contains Chars).

source
UnROOT.TH — Method
TH(io, tkey::TKey, refs)

Internal function used to form a fields = Dict{Symbol, Any}() that represents the fields of a TH (histogram) in C++ ROOT.

source
UnROOT._field_output_type — Method
_field_output_type(::Type{F}) where F

This is function is used in two ways:

  • provide a output type prediction for each "field" in RNTuple so we can

achieve type stability

  • it's also used to enforce the type stability in read_field:
    # this is basically a type assertion for `res`
+    return res::_field_output_type(field)
source
UnROOT.array — Method
array(f::ROOTFile, path; raw=false)

Reads an array from a branch. Set raw=true to return raw data and correct offsets.

source
UnROOT.auto_T_JaggT — Method
auto_T_JaggT(f::ROOTFile, branch; customstructs::Dict{String, Type})

Given a file and branch, automatically return (eltype, Jaggtype). This function is aware of custom structs that are carried with the parent ROOTFile.

This is also where you may want to "redirect" classname -> Julia struct name, for example "TLorentzVector" => LorentzVector here and you can focus on LorentzVectors.LorentzVector methods from here on.

See also: ROOTFile, interped_data

source
UnROOT.basketarray — Method
basketarray(f::ROOTFile, path::AbstractString, ith)
+basketarray(f::ROOTFile, branch::Union{TBranch, TBranchElement}, ith)
+basketarray(lb::LazyBranch, ith)

Reads actual data from ith basket of a branch. This function first calls readbasket to obtain raw bytes and offsets of a basket, then calls auto_T_JaggT followed by interped_data to translate raw bytes into actual data.

source
UnROOT.basketarray_iter — Method
basketarray_iter(f::ROOTFile, branch::Union{TBranch, TBranchElement})
+basketarray_iter(lb::LazyBranch)

Returns a Base.Generator yielding the output of basketarray() for all baskets.

source
UnROOT.chaintrees — Method
chaintrees(ts)

Chain a collection of LazyTrees together to form a larger tree, every tree should have identical branch names and types, we're not trying to re-implement SQL here.

Example

julia> typeof(tree)
+LazyTree with 1 branches:
+a
+
+julia> tree2 = UnROOT.chaintrees([tree,tree]);
+
+julia> eltype(tree.a) == eltype(tree2.a)
+true
+
+julia> length(tree)
+100
+
+julia> length(tree2)
+200
+
+julia> eltype(tree)
+UnROOT.LazyEvent{NamedTuple{(:a,), Tuple{LazyBranch{Int32, UnROOT.Nojagg, Vector{Int32}}}}}
+
+julia> eltype(tree2)
+UnROOT.LazyEvent{NamedTuple{(:a,), Tuple{SentinelArrays.ChainedVector{Int32, LazyBranch{Int32, UnROOT.Nojagg, Vector{Int32}}}}}}
source
UnROOT.decompress_datastreambytes — Method
decompress_datastreambytes(compbytes, tkey)

Process the compressed bytes compbytes which was read out by compressed_datastream and pointed to from tkey. This function simply return uncompressed bytes according to the compression algorithm detected (or the lack of).

source
UnROOT.endcheck — Method
function endcheck(io, preamble::Preamble)

Checks if everything went well after parsing a TOBject. Used in conjuction with Preamble.

source
UnROOT.interped_data — Method
interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{J}) where {T, J<:JaggType}

The function thats interpret raw bytes (from a basket) into corresponding Julia data, based on type T and jagg type J.

In order to retrieve data from custom branches, user should defined more speialized method of this function with specific T and J. See TLorentzVector example.

source
UnROOT.interped_data — Method
interped_data(rawdata, rawoffsets, ::Type{Vector{LorentzVector{Float64}}}, ::Type{Offsetjagg})

The interped_data method specialized for LorentzVector. This method will get called by basketarray instead of the default method for TLorentzVector branch.

source
UnROOT.parseTH — Method
parseTH(th::Dict{Symbol, Any})

Parse the output of TH into a tuple of counts, edges, and sumw2. A StatsBase.Histogram can then be constructed with Histogram(edges, counts). TH1 and TH2 inputs are supported.

source
UnROOT.parsetobject — Method

Direct parsing of streamed objects which are not sitting on branches. This function needs to be rewritten, so that it can create proper types of TObject inherited data (like TVectorT<*>).

source
UnROOT.read_field — Method
read_field(io, field::F, page_list) where F

Read a field from the io stream. The page_list is a list of PageLinks for the current cluster group. The type stability is achieved by type asserting based on type F via _field_output_type function.

source
UnROOT.read_field — Method
read_field(io, field::StructField{N, T}, page_list) where {N, T}

Since each field of the struct is stored in a separate field of the RNTuple, this function returns a StructArray to maximize efficiency.

source
UnROOT.read_pagedesc — Method
read_pagedesc(io, pagedesc::Vector{PageDescription}, nbits::Integer)

Read the decompressed raw bytes given a Page Description. The nbits need to be provided according to the element type of the column since pagedesc only contains num_elements information.

Note

Boolean values are always stored as bit in RNTuple, so nbits = 1.

source
UnROOT.readbasket — Method
readbasket(f::ROOTFile, branch, ith)
+readbasketseek(f::ROOTFile, branch::Union{TBranch, TBranchElement}, seek_pos::Int, nbytes)

The fundamental building block of reading read data from a .root file. Read read one basket's raw bytes and offsets at a time. These raw bytes and offsets then (potentially) get processed by interped_data.

See also: auto_T_JaggT, basketarray

source
UnROOT.readobjany! — Method
function readobjany!(io, tkey::TKey, refs)

The main entrypoint where streamers are parsed and cached for later use. The refs dictionary holds the streamers or parsed data which are reused when already available.

source
UnROOT.splitup — Method
splitup(data::Vector{UInt8}, offsets, T::Type; skipbytes=0)

Given the offsets and data return by array(...; raw = true), reconstructed the actual array (with custome struct, can be jagged as well).

source
UnROOT.topological_sort — Method
function topological_sort(streamer_infos)

Sort the streamers with respect to their dependencies and keep only those which are not defined already.

The implementation is based on https://stackoverflow.com/a/11564769/1623645

source
UnROOT.unpack — Method
unpack(x::CompressionHeader)

Return the following information:

  • Name of compression algorithm
  • Level of the compression
  • compressedbytes and uncompressedbytes according to uproot3
source
UnROOT.@SimpleStruct — Macro
macro SimpleStruct

Define reading method on the fly for _rntuple_read

Example

julia> @SimpleStruct struct Locator
+           num_bytes::Int32
+           offset::UInt64
+       end

would automatically define the following reading method:

function _rntuple_read(io, ::Type{Locator})
+    num_bytes = _rntuple_read(io, Int32)
+    offset = _rntuple_read(io, UInt64)
+    Locator(num_bytes, offset)
+end

Notice _rntuple_read falls back to read for all types that are not defined by us.

source
UnROOT.@stack — Macro
macro stack(into, structs...)

Stack the fields of multiple structs and create a new one. The first argument is the name of the new struct followed by the ones to be stacked. Parametric types are not supported and the fieldnames needs to be unique.

Example:

@stack Baz Foo Bar

Creates Baz with the concatenated fields of Foo and Bar

source
diff --git a/previews/PR276/performancetips/index.html b/previews/PR276/performancetips/index.html new file mode 100644 index 00000000..cdaced13 --- /dev/null +++ b/previews/PR276/performancetips/index.html @@ -0,0 +1,9 @@ + +Performance Tips · UnROOT.jl

Don't "double access"

Inside an event-loop:

for evt in mytree
+    evt.nMuon!=4 && continue
+    calculation(evt.nMuon)
+end

This is bad practice. Since evt is a lazy construct, read happens when you access a property by e.g. evt.nMuon. This means that if you need a branch multiple times, you should allocate a variable first:

for evt in mytree
+    nmu = evt.nMuon
+    nmu !=4 && continue
+    calculation(nmu)
+end
diff --git a/previews/PR276/search_index.js b/previews/PR276/search_index.js new file mode 100644 index 00000000..b69dad8c --- /dev/null +++ b/previews/PR276/search_index.js @@ -0,0 +1,3 @@ +var documenterSearchIndex = {"docs": +[{"location":"internalapis/#Commonly-used","page":"APIs","title":"Commonly used","text":"","category":"section"},{"location":"internalapis/","page":"APIs","title":"APIs","text":"Modules = [UnROOT]\nFilter = t -> contains(string(t), \"Lazy\")","category":"page"},{"location":"internalapis/#UnROOT.LazyBranch","page":"APIs","title":"UnROOT.LazyBranch","text":"LazyBranch(f::ROOTFile, branch)\n\nConstruct an accessor for a given branch such that BA[idx] and or BA[1:20] is type-stable. And memory footprint is a single basket (<1MB usually). You can also iterate or map over it. If you want a concrete Vector, simply collect() the LazyBranch.\n\nExample\n\njulia> rf = ROOTFile(\"./test/samples/tree_with_large_array.root\");\n\njulia> b = rf[\"t1/int32_array\"];\n\njulia> ab = UnROOT.LazyBranch(rf, b);\n\njulia> for entry in ab\n @show entry\n break\n end\nentry = 0\n\njulia> ab[begin:end]\n0\n1\n...\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.LazyTree-Tuple{ROOTFile, AbstractString, Any}","page":"APIs","title":"UnROOT.LazyTree","text":"LazyTree(f::ROOTFile, s::AbstractString, branche::Union{AbstractString, Regex})\nLazyTree(f::ROOTFile, s::AbstractString, branches::Vector{Union{AbstractString, Regex}})\n\nConstructor for LazyTree, which is close to an DataFrame (interface wise), and a lazy Table (speed wise). Looping over a LazyTree is fast and type stable. Internally, LazyTree contains a typed table whose branch are LazyBranch. This means that at any given time only N baskets are cached, where N is the number of branches.\n\nnote: Note\nAccessing with [start:stop] will return a LazyTree with concrete internal table.\n\nwarning: Warning\nSplit branches are re-named, and the exact renaming may change. See Issue 156 for context.\n\nExample\n\njulia> mytree = LazyTree(f, \"Events\", [\"Electron_dxy\", \"nMuon\", r\"Muon_(pt|eta)$\"])\n Row │ Electron_dxy nMuon Muon_eta Muon_pt\n │ Vector{Float32} UInt32 Vector{Float32} Vector{Float32}\n─────┼───────────────────────────────────────────────────────────\n 1 │ [0.000371] 0 [] []\n 2 │ [-0.00982] 2 [0.53, 0.229] [19.9, 15.3]\n 3 │ [] 0 [] []\n 4 │ [-0.00157] 0 [] []\n ⋮ │ ⋮ ⋮ ⋮ ⋮\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.LazyTree-Tuple{ROOTFile, UnROOT.TTree, Any, Any}","page":"APIs","title":"UnROOT.LazyTree","text":"function LazyTree(f::ROOTFile, tree::TTree, treepath, branches)\n\nCreates a lazy tree object of the selected branches only. branches is vector of String, Regex or Pair{Regex, SubstitutionString}, where the first item is the regex selector and the second item the rename pattern.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#More-Internal","page":"APIs","title":"More Internal","text":"","category":"section"},{"location":"internalapis/","page":"APIs","title":"APIs","text":"Modules = [UnROOT]\nFilter = t -> !(contains(string(t), \"Lazy\"))","category":"page"},{"location":"internalapis/#UnROOT.Cursor","page":"APIs","title":"UnROOT.Cursor","text":"The Cursor type is embeded into Branches of a TTree such that when we need to read the content of a Branch, we don't need to go through the Directory and find the TKey and then seek to where the Branch is.\n\nnote: Note\nThe io inside a Cursor is in fact only a buffer, it is NOT a io that refers to the whole file's stream.\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.LeafField","page":"APIs","title":"UnROOT.LeafField","text":"struct LeafField{T}\n content_col_idx::Int\n type::Int\n nbits::Int\nend\n\nBase case of field nesting, this links to a column in the RNTuple by 0-based index. T is the eltype of this field which mostly uses Julia native types except for Switch.\n\nThe type field is the RNTuple spec type number, used to record split encoding.\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.OffsetBuffer","page":"APIs","title":"UnROOT.OffsetBuffer","text":"OffsetBuffer\n\nWorks with seek, position of the original file. Think of it as a view of IOStream that can be indexed with original positions.\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.Preamble-Union{Tuple{T}, Tuple{Any, Type{T}}} where T","page":"APIs","title":"UnROOT.Preamble","text":"Reads the preamble of an object.\n\nThe cursor will be put into the right place depending on the data.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.RNTuple","page":"APIs","title":"UnROOT.RNTuple","text":"RNTuple\n\nThis is the struct for holding all metadata (schema) needed to completely describe and RNTuple from ROOT, just like TTree, to obtain a table-like data object, you need to use LazyTree explicitly:\n\nExample\n\njulia> f = ROOTFile(\"./test/samples/RNTuple/test_ntuple_stl_containers.root\");\n\njulia> f[\"ntuple\"]\nUnROOT.RNTuple:\n header:\n name: \"ntuple\"\n ntuple_description: \"\"\n writer_identifier: \"ROOT v6.29/01\"\n schema:\n RNTupleSchema with 13 top fields\n ├─ :lorentz_vector ⇒ Struct\n ├─ :vector_tuple_int32_string ⇒ Vector\n ├─ :string ⇒ String\n ├─ :vector_string ⇒ Vector\n...\n..\n.\n\njulia> LazyTree(f, \"ntuple\")\n Row │ string vector_int32 array_float vector_vector_i vector_string vector_vector_s variant_int32_s vector_variant_ ⋯\n │ String Vector{Int32} StaticArraysCor Vector{Vector{I Vector{String} Vector{Vector{S Union{Int32, St Vector{Union{In ⋯\n─────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────\n 1 │ one [1] [1.0, 1.0, 1.0] Vector{Int32}[Int3 [\"one\"] [[\"one\"]] 1 Union{Int64, Strin ⋯\n 2 │ two [1, 2] [2.0, 2.0, 2.0] Vector{Int32}[Int3 [\"one\", \"two\"] [[\"one\"], [\"two\"]] two Union{Int64, Strin ⋯\n 3 │ three [1, 2, 3] [3.0, 3.0, 3.0] Vector{Int32}[Int3 [\"one\", \"two\", \"th [[\"one\"], [\"two\"], three Union{Int64, Strin ⋯\n 4 │ four [1, 2, 3, 4] [4.0, 4.0, 4.0] Vector{Int32}[Int3 [\"one\", \"two\", \"th [[\"one\"], [\"two\"], 4 Union{Int64, Strin ⋯\n 5 │ five [1, 2, 3, 4, 5] [5.0, 5.0, 5.0] Vector{Int32}[Int3 [\"one\", \"two\", \"th [[\"one\"], [\"two\"], 5 Union{Int64, Strin ⋯\n 5 columns omitted\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.RNTupleCardinality","page":"APIs","title":"UnROOT.RNTupleCardinality","text":"struct RNTupleCardinality{T}\n content_col_idx::Int\n nbits::Int\nend\n\nSpecial field. The cardinality is basically a counter, but the data column is a leaf column of Index32 or Index64. To get a number from Cardinality, one needs to compute ary[i] - ary[i-1].\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.RNTupleField","page":"APIs","title":"UnROOT.RNTupleField","text":"mutable struct RNTupleField{R, F, O, E} <: AbstractVector{E}\n\nNot a counterpart of RNTuple field in ROOT. This is a user-facing Julia-only construct like LazyBranch that is meant to act like a lazy AbstractVector backed with file IO source and a schema field from RNTuple.schema.\n\nR is the type of parent RNTuple\nF is the type of the field in the schema\n'O' is the type of output when you read a cluster-worth of data\n'E' is the element type of O (i.e. what you get for each event (row) in iteration)\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.RNTupleSchema","page":"APIs","title":"UnROOT.RNTupleSchema","text":"struct RNTupleSchema\n\nA wrapper struct for print_tree implementation of the schema display.\n\nExample\n\njulia> f = ROOTFile(\"./test/samples/RNTuple/test_ntuple_stl_containers.root\");\n\njulia> f[\"ntuple\"].schema\nRNTupleSchema with 13 top fields\n├─ :lorentz_vector ⇒ Struct\n│ ├─ :pt ⇒ Leaf{Float32}(col=26)\n│ ├─ :eta ⇒ Leaf{Float32}(col=27)\n│ ├─ :phi ⇒ Leaf{Float32}(col=28)\n│ └─ :mass ⇒ Leaf{Float32}(col=29)\n├─ :vector_tuple_int32_string ⇒ Vector\n│ ├─ :offset ⇒ Leaf{Int32}(col=9)\n│ └─ :content ⇒ Struct\n│ ├─ :_1 ⇒ String\n│ │ ├─ :offset ⇒ Leaf{Int32}(col=37)\n│ │ └─ :content ⇒ Leaf{Char}(col=38)\n│ └─ :_0 ⇒ Leaf{Int32}(col=36)\n├─ :string ⇒ String\n│ ├─ :offset ⇒ Leaf{Int32}(col=1)\n│ └─ :content ⇒ Leaf{Char}(col=2)\n├─ :vector_string ⇒ Vector\n│ ├─ :offset ⇒ Leaf{Int32}(col=5)\n│ └─ :content ⇒ String\n│ ├─ :offset ⇒ Leaf{Int32}(col=13)\n│ └─ :content ⇒ Leaf{Char}(col=14)\n...\n..\n.\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.ROOTFile-Tuple{AbstractString}","page":"APIs","title":"UnROOT.ROOTFile","text":"ROOTFile(filename::AbstractString; customstructs = Dict(\"TLorentzVector\" => LorentzVector{Float64}))\n\nROOTFile's constructor from a file. The customstructs dictionary can be used to pass user-defined struct as value and its corresponding fClassName (in Branch) as key such that UnROOT will know to intepret them, see interped_data.\n\nSee also: LazyTree, LazyBranch\n\nExample\n\njulia> f = ROOTFile(\"test/samples/NanoAODv5_sample.root\")\nROOTFile with 2 entries and 21 streamers.\ntest/samples/NanoAODv5_sample.root\n└─ Events\n ├─ \"run\"\n ├─ \"luminosityBlock\"\n ├─ \"event\"\n ├─ \"HTXS_Higgs_pt\"\n ├─ \"HTXS_Higgs_y\"\n └─ \"⋮\"\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.StdArrayField","page":"APIs","title":"UnROOT.StdArrayField","text":"StdArrayField\n\nSpecial base-case field for a leaf field representing std::array. This is because RNTuple would serialize it as a leaf field but with flags == 0x0001 in the field description. In total, there are two field descriptions associlated with array<>, one for meta-data (the N), the other one for the actual data.\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.Streamers-Tuple{Any}","page":"APIs","title":"UnROOT.Streamers","text":"function Streamers(io)\n\nReads all the streamers from the ROOT source.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.StringField","page":"APIs","title":"UnROOT.StringField","text":"StringField\n\nSpecial base-case field for String leaf field. This is because RNTuple splits a leaf String field into two columns (instead of split in field records). So we need an offset column and a content column (that contains Chars).\n\n\n\n\n\n","category":"type"},{"location":"internalapis/#UnROOT.TH-Tuple{Any, Union{UnROOT.TKey32, UnROOT.TKey64}, Any}","page":"APIs","title":"UnROOT.TH","text":"TH(io, tkey::TKey, refs)\n\nInternal function used to form a fields = Dict{Symbol, Any}() that represents the fields of a TH (histogram) in C++ ROOT.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT._field_output_type-Tuple{}","page":"APIs","title":"UnROOT._field_output_type","text":"_field_output_type(::Type{F}) where F\n\nThis is function is used in two ways:\n\nprovide a output type prediction for each \"field\" in RNTuple so we can\n\nachieve type stability\n\nit's also used to enforce the type stability in read_field:\n\n # this is basically a type assertion for `res`\n return res::_field_output_type(field)\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT._rntuple_clusterrange-Tuple{UnROOT.ClusterSummary}","page":"APIs","title":"UnROOT._rntuple_clusterrange","text":"The event number range a given cluster covers, in Julia's index\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.array-Tuple{ROOTFile, AbstractString}","page":"APIs","title":"UnROOT.array","text":"array(f::ROOTFile, path; raw=false)\n\nReads an array from a branch. Set raw=true to return raw data and correct offsets.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.arrays-Tuple{ROOTFile, Any}","page":"APIs","title":"UnROOT.arrays","text":"arrays(f::ROOTFile, treename)\n\nReads all branches from a tree.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.auto_T_JaggT-Tuple{ROOTFile, Any}","page":"APIs","title":"UnROOT.auto_T_JaggT","text":"auto_T_JaggT(f::ROOTFile, branch; customstructs::Dict{String, Type})\n\nGiven a file and branch, automatically return (eltype, Jaggtype). This function is aware of custom structs that are carried with the parent ROOTFile.\n\nThis is also where you may want to \"redirect\" classname -> Julia struct name, for example \"TLorentzVector\" => LorentzVector here and you can focus on LorentzVectors.LorentzVector methods from here on.\n\nSee also: ROOTFile, interped_data\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.basketarray-Tuple{ROOTFile, AbstractString, Any}","page":"APIs","title":"UnROOT.basketarray","text":"basketarray(f::ROOTFile, path::AbstractString, ith)\nbasketarray(f::ROOTFile, branch::Union{TBranch, TBranchElement}, ith)\nbasketarray(lb::LazyBranch, ith)\n\nReads actual data from ith basket of a branch. This function first calls readbasket to obtain raw bytes and offsets of a basket, then calls auto_T_JaggT followed by interped_data to translate raw bytes into actual data.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.basketarray_iter-Tuple{ROOTFile, Any}","page":"APIs","title":"UnROOT.basketarray_iter","text":"basketarray_iter(f::ROOTFile, branch::Union{TBranch, TBranchElement})\nbasketarray_iter(lb::LazyBranch)\n\nReturns a Base.Generator yielding the output of basketarray() for all baskets.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.chaintrees-Tuple{Any}","page":"APIs","title":"UnROOT.chaintrees","text":"chaintrees(ts)\n\nChain a collection of LazyTrees together to form a larger tree, every tree should have identical branch names and types, we're not trying to re-implement SQL here.\n\nExample\n\njulia> typeof(tree)\nLazyTree with 1 branches:\na\n\njulia> tree2 = UnROOT.chaintrees([tree,tree]);\n\njulia> eltype(tree.a) == eltype(tree2.a)\ntrue\n\njulia> length(tree)\n100\n\njulia> length(tree2)\n200\n\njulia> eltype(tree)\nUnROOT.LazyEvent{NamedTuple{(:a,), Tuple{LazyBranch{Int32, UnROOT.Nojagg, Vector{Int32}}}}}\n\njulia> eltype(tree2)\nUnROOT.LazyEvent{NamedTuple{(:a,), Tuple{SentinelArrays.ChainedVector{Int32, LazyBranch{Int32, UnROOT.Nojagg, Vector{Int32}}}}}}\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.compressed_datastream-Tuple{Any, Any}","page":"APIs","title":"UnROOT.compressed_datastream","text":"compressed_datastream(io, tkey)\n\nExtract all [compressionheader][rawbytes] from a TKey. This is an isolated function because we want to compartmentalize disk I/O as much as possible.\n\nSee also: decompress_datastreambytes\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.decompress_datastreambytes-Tuple{Any, Any}","page":"APIs","title":"UnROOT.decompress_datastreambytes","text":"decompress_datastreambytes(compbytes, tkey)\n\nProcess the compressed bytes compbytes which was read out by compressed_datastream and pointed to from tkey. This function simply return uncompressed bytes according to the compression algorithm detected (or the lack of).\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.endcheck-Union{Tuple{T}, Tuple{Any, T}} where T<:UnROOT.Preamble","page":"APIs","title":"UnROOT.endcheck","text":"function endcheck(io, preamble::Preamble)\n\nChecks if everything went well after parsing a TOBject. Used in conjuction with Preamble.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.interped_data-Tuple{Any, Any, Type{Bool}, Type{UnROOT.Nojagg}}","page":"APIs","title":"UnROOT.interped_data","text":"interped_data(rawdata, rawoffsets, ::Type{T}, ::Type{J}) where {T, J<:JaggType}\n\nThe function thats interpret raw bytes (from a basket) into corresponding Julia data, based on type T and jagg type J.\n\nIn order to retrieve data from custom branches, user should defined more speialized method of this function with specific T and J. See TLorentzVector example.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.interped_data-Tuple{Any, Any, Type{Vector{LorentzVectors.LorentzVector{Float64}}}, Type{UnROOT.Offsetjagg}}","page":"APIs","title":"UnROOT.interped_data","text":"interped_data(rawdata, rawoffsets, ::Type{Vector{LorentzVector{Float64}}}, ::Type{Offsetjagg})\n\nThe interped_data method specialized for LorentzVector. This method will get called by basketarray instead of the default method for TLorentzVector branch.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.parseTH-Tuple{Dict{Symbol, Any}}","page":"APIs","title":"UnROOT.parseTH","text":"parseTH(th::Dict{Symbol, Any})\n\nParse the output of TH into a tuple of counts, edges, and sumw2. A StatsBase.Histogram can then be constructed with Histogram(edges, counts). TH1 and TH2 inputs are supported.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.parsetobject-Tuple{Any, Union{UnROOT.TKey32, UnROOT.TKey64}, Any}","page":"APIs","title":"UnROOT.parsetobject","text":"Direct parsing of streamed objects which are not sitting on branches. This function needs to be rewritten, so that it can create proper types of TObject inherited data (like TVectorT<*>).\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.read_field-Tuple{}","page":"APIs","title":"UnROOT.read_field","text":"read_field(io, field::F, page_list) where F\n\nRead a field from the io stream. The page_list is a list of PageLinks for the current cluster group. The type stability is achieved by type asserting based on type F via _field_output_type function.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.read_field-Union{Tuple{T}, Tuple{N}, Tuple{Any, UnROOT.StructField{N, T}, Any}} where {N, T}","page":"APIs","title":"UnROOT.read_field","text":"read_field(io, field::StructField{N, T}, page_list) where {N, T}\n\nSince each field of the struct is stored in a separate field of the RNTuple, this function returns a StructArray to maximize efficiency.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.read_pagedesc-Tuple{Any, Vector{UnROOT.PageDescription}, Integer}","page":"APIs","title":"UnROOT.read_pagedesc","text":"read_pagedesc(io, pagedesc::Vector{PageDescription}, nbits::Integer)\n\nRead the decompressed raw bytes given a Page Description. The nbits need to be provided according to the element type of the column since pagedesc only contains num_elements information.\n\nnote: Note\nBoolean values are always stored as bit in RNTuple, so nbits = 1.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.readbasket-Tuple{ROOTFile, Any, Any}","page":"APIs","title":"UnROOT.readbasket","text":"readbasket(f::ROOTFile, branch, ith)\nreadbasketseek(f::ROOTFile, branch::Union{TBranch, TBranchElement}, seek_pos::Int, nbytes)\n\nThe fundamental building block of reading read data from a .root file. Read read one basket's raw bytes and offsets at a time. These raw bytes and offsets then (potentially) get processed by interped_data.\n\nSee also: auto_T_JaggT, basketarray\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.readobjany!-Tuple{Any, Union{UnROOT.TKey32, UnROOT.TKey64}, Any}","page":"APIs","title":"UnROOT.readobjany!","text":"function readobjany!(io, tkey::TKey, refs)\n\nThe main entrypoint where streamers are parsed and cached for later use. The refs dictionary holds the streamers or parsed data which are reused when already available.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.skiptobj-Tuple{Any}","page":"APIs","title":"UnROOT.skiptobj","text":"function skiptobj(io)\n\nSkips a TOBject.\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.splitup-Tuple{Vector{UInt8}, Any, Type}","page":"APIs","title":"UnROOT.splitup","text":"splitup(data::Vector{UInt8}, offsets, T::Type; skipbytes=0)\n\nGiven the offsets and data return by array(...; raw = true), reconstructed the actual array (with custome struct, can be jagged as well).\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.topological_sort-Tuple{Any}","page":"APIs","title":"UnROOT.topological_sort","text":"function topological_sort(streamer_infos)\n\nSort the streamers with respect to their dependencies and keep only those which are not defined already.\n\nThe implementation is based on https://stackoverflow.com/a/11564769/1623645\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.unpack-Tuple{UnROOT.CompressionHeader}","page":"APIs","title":"UnROOT.unpack","text":"unpack(x::CompressionHeader)\n\nReturn the following information:\n\nName of compression algorithm\nLevel of the compression\ncompressedbytes and uncompressedbytes according to uproot3\n\n\n\n\n\n","category":"method"},{"location":"internalapis/#UnROOT.@SimpleStruct-Tuple{Any}","page":"APIs","title":"UnROOT.@SimpleStruct","text":"macro SimpleStruct\n\nDefine reading method on the fly for _rntuple_read\n\nExample\n\njulia> @SimpleStruct struct Locator\n num_bytes::Int32\n offset::UInt64\n end\n\nwould automatically define the following reading method:\n\nfunction _rntuple_read(io, ::Type{Locator})\n num_bytes = _rntuple_read(io, Int32)\n offset = _rntuple_read(io, UInt64)\n Locator(num_bytes, offset)\nend\n\nNotice _rntuple_read falls back to read for all types that are not defined by us.\n\n\n\n\n\n","category":"macro"},{"location":"internalapis/#UnROOT.@stack-Tuple{Any, Vararg{Any}}","page":"APIs","title":"UnROOT.@stack","text":"macro stack(into, structs...)\n\nStack the fields of multiple structs and create a new one. The first argument is the name of the new struct followed by the ones to be stacked. Parametric types are not supported and the fieldnames needs to be unique.\n\nExample:\n\n@stack Baz Foo Bar\n\nCreates Baz with the concatenated fields of Foo and Bar\n\n\n\n\n\n","category":"macro"},{"location":"advanced/custom_branch/#Parse-Custom-Branch","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"","category":"section"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"It is possible to parse Branches with custom structure as long as you know how the bytes should be interpreted. As an example, the TLorentzVector is added using this mechanism and we will walk through the steps needed:","category":"page"},{"location":"advanced/custom_branch/#.-Provide-a-map-between-fClassName-of-your-struct-(as-seen-in-.root)-to-a-Julia-type.","page":"Parse Custom Branch","title":"1. Provide a map between fClassName of your struct (as seen in .root) to a Julia type.","text":"","category":"section"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"Pass a Dict{String, Type} to ROOTFile(filepath; customstructs). The TLorentzVector is shipped by default:","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"ROOTFile(filepath; customstructs = Dict(\"TLorentzVector\" => LorentzVector{Float64}))","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"This Dict will subsequently be used by the auto_T_JaggT function at here such that when we encounter a branch with this fClassName, we will return your Type as the detected element type of this branch.","category":"page"},{"location":"advanced/custom_branch/#.-Extend-the-raw-bytes-interpreting-function-UnROOT.interped_data","page":"Parse Custom Branch","title":"2. Extend the raw bytes interpreting function UnROOT.interped_data","text":"","category":"section"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"By default, given a branch element type and a \"jaggness\" type, a general function is defined which will try to parse the raw bytes into Julia data structure. The ::Type{T} will match what you have provided in the Dict in the previous step.","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"Thus, to \"teach\" UnROOT how to interpret bytes for your type T, you would want to defined a more specific UnROOT.interped_data than the default one. Taking the TLorentzVector as example again, we define a function:","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"using LorentzVector\nconst LVF64 = LorentzVector{Float64}\nfunction UnROOT.interped_data(rawdata, rawoffsets, ::Type{LVF64}, ::Type{J}) where {T, J <: JaggType}\n # `rawoffsets` is actually redundant, since we know each TLV is always 64 bytes (withe 32 bytes header)\n [\n reinterpret(LVF64, x) for x in Base.Iterators.partition(rawdata, 64)\n ]\nend\n\n# VorView is defined in the `src/custom.jl`\nfunction Base.reinterpret(::Type{LVF64}, v::VorView) where T\n # x,y,z,t in ROOT\n v4 = ntoh.(reinterpret(Float64, v[1+32:end]))\n # t,x,y,z in LorentzVectors.jl\n LVF64(v4[4], v4[1], v4[2], v4[3])\nend","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"The Base.reinterpret function is just a helper function, you could instead write everything inside UnROOT.interped_data. We then builds on these, to interpret Jagged TLV branch: https://github.com/JuliaHEP/UnROOT.jl/blob/4747f6f5fd97ed1a872765485b4eb9e99ec5a650/src/custom.jl#L47","category":"page"},{"location":"advanced/custom_branch/#More-details","page":"Parse Custom Branch","title":"More details","text":"","category":"section"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"To expand a bit what we're doing here, the rawdata for a single TLV is always 64 bytes long and the first 32 bytes are TObject header which we don't care (which is why we don't care about rawoffsets here). The last 32 bytes make up 4 Float64 and we simply parse them and return a collection of (julia) LorentzVector{Float64}.","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"In general, if auto_T_JaggT returned MyType as promised branch element type, then","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"UnROOT.interped_data(rawdata, rawoffsets, ::Type{MyType},","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"should return Vector{MyType} because UnROOT.interped_data receives raw bytes of a basket at a time.","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"And that's it! Afterwards both LazyBranch and LazyTree will be able to constructed with correct type and also knows how to interpret bytes when you indexing or iterating through them","category":"page"},{"location":"advanced/custom_branch/#Reading-Raw-Data-from-Branch","page":"Parse Custom Branch","title":"Reading Raw Data from Branch","text":"","category":"section"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"Alternatively, reading raw data is also possible using the UnROOT.array(f::ROOTFile, path; raw=true) method. The output can be then reinterpreted using a custom type with the method UnROOT.splitup(data, offsets, T::Type; skipbytes=0, jagged=true). This provides more fine grain control in case your branch is highly irregular. You can then define suitable Julia type and readtype method for parsing these data. Alternatively, you can of course parse the data and offsets entirely manually. Here is it in action, with the help of the types from custom.jl, and some data from the KM3NeT experiment:","category":"page"},{"location":"advanced/custom_branch/","page":"Parse Custom Branch","title":"Parse Custom Branch","text":"julia> using UnROOT\n\njulia> f = ROOTFile(\"test/samples/km3net_online.root\")\nROOTFile(\"test/samples/km3net_online.root\") with 10 entries and 41 streamers.\n\njulia> data, offsets = array(f, \"KM3NET_EVENT/KM3NET_EVENT/snapshotHits\"; raw=true)\n2058-element Array{UInt8,1}:\n 0x00\n 0x03\n ⋮\n \njulia> UnROOT.splitup(data, offsets, UnROOT._KM3NETDAQHit)\n4-element Vector{Vector{UnROOT._KM3NETDAQHit}}:\n [UnROOT._KM3NETDAQHit(1073742790, 0x00, 9, 0x60)......","category":"page"},{"location":"performancetips/#Don't-\"double-access\"","page":"Performance Tips","title":"Don't \"double access\"","text":"","category":"section"},{"location":"performancetips/","page":"Performance Tips","title":"Performance Tips","text":"Inside an event-loop:","category":"page"},{"location":"performancetips/","page":"Performance Tips","title":"Performance Tips","text":"for evt in mytree\n evt.nMuon!=4 && continue\n calculation(evt.nMuon)\nend","category":"page"},{"location":"performancetips/","page":"Performance Tips","title":"Performance Tips","text":"This is bad practice. Since evt is a lazy construct, read happens when you access a property by e.g. evt.nMuon. This means that if you need a branch multiple times, you should allocate a variable first:","category":"page"},{"location":"performancetips/","page":"Performance Tips","title":"Performance Tips","text":"for evt in mytree\n nmu = evt.nMuon\n nmu !=4 && continue\n calculation(nmu)\nend","category":"page"},{"location":"exampleusage/#Chunk-Iteration","page":"Example Usage","title":"Chunk Iteration","text":"","category":"section"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"t = LazyTree(...)\nres = 0.0\nfor rang in Iterators.partition(1:lastindex(t), 10^6)\n res += sum(t[rang].nMuon) #\nend\nres","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"Note, t[rang] is eager, if you don't need all branches, it's much better to use t.nMuon[rang], or limit which branches are selected during LazyTree() creation time.","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"This pattern works the best over network, for local files, stick with:","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"for evt in t\n ...\nend","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"usually is the best approach.","category":"page"},{"location":"exampleusage/#Writting-out-.root-files","page":"Example Usage","title":"Writting out .root files","text":"","category":"section"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"Currently UnROOT.jl is focused on reading only, however, it's semi-trivial to leverage Python world for write operation since it's not performance critical.","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"You have the following choice:","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"PythonCall.jl – we will demo how to use this one\nPyCall.jl","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"Checkout configuration docs for PythonCall.jl","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"Most importantly, you probably want to set:","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"ENV[\"JULIA_PYTHONCALL_EXE\"] = readchomp(`which python`)","category":"page"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"before the using PythonCall line. Especially if you're using LCG or Athena or CMSSW environment.","category":"page"},{"location":"exampleusage/#Write-out-a-TTree","page":"Example Usage","title":"Write out a TTree","text":"","category":"section"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"julia> using PythonCall\n\njulia> const up = pyimport(\"uproot\")\n\njulia> pywith(up.recreate(\"./example.root\")) do file\n file[\"mytree\"] = Dict(\"branch1\"=>1:1000, \"branch2\"=>rand(1000))\n end\n\n# read it back with UnROOT.jl\njulia> using UnROOT\n\njulia> LazyTree(\"./example.root\", \"mytree\")\n Row │ branch1 branch2 \n │ Int64 Float64 \n─────┼───────────────────────────────\n 1 │ 1 0.5775868298287866\n 2 │ 2 0.7245212475492369\n 3 │ 3 0.009249240901789912\n 4 │ 4 0.9010206670973542\n 5 │ 5 0.7609879879740359\n 6 │ 6 0.00916447384387542\n 7 │ 7 0.5636229077934333\n 8 │ 8 0.32617388561103156\n ⋮ │ ⋮ ⋮","category":"page"},{"location":"exampleusage/#Write-out-a-histogram","page":"Example Usage","title":"Write out a histogram","text":"","category":"section"},{"location":"exampleusage/","page":"Example Usage","title":"Example Usage","text":"A histogram is just a tuple of (bincontent, binedges), see FHist.jl docs for details.","category":"page"},{"location":"advanced/reduce_latency/#Bake-sysimage-with-PackageCompiler.jl","page":"Reduce startup latency","title":"Bake sysimage with PackageCompiler.jl","text":"","category":"section"},{"location":"advanced/reduce_latency/","page":"Reduce startup latency","title":"Reduce startup latency","text":"You can bake a sysimage tailored for your analysis to reduce latency.","category":"page"},{"location":"advanced/reduce_latency/","page":"Reduce startup latency","title":"Reduce startup latency","text":"> cat readtree.jl\nusing UnROOT\n\nconst r = ROOTFile(\"/home/akako/.julia/dev/UnROOT/test/samples/NanoAODv5_sample.root\")\n\nconst t = LazyTree(r, \"Events\", [\"nMuon\", \"Electron_dxy\"])\n\n\n@show t[1, :Electron_dxy]\n\n> time julia --startup-file=no readtree.jl\nt[1, :Electron_dxy] = Float32[0.00037050247]\n\n________________________________________________________\nExecuted in 10.82 secs fish external\n usr time 11.09 secs 580.00 micros 11.09 secs\n sys time 0.65 secs 189.00 micros 0.65 secs","category":"page"},{"location":"advanced/reduce_latency/","page":"Reduce startup latency","title":"Reduce startup latency","text":"In Julia, `]add PackageCompiler':","category":"page"},{"location":"advanced/reduce_latency/","page":"Reduce startup latency","title":"Reduce startup latency","text":"julia> using PackageCompiler\n\njulia> PackageCompiler.create_sysimage(:UnROOT; precompile_statements_file=\"./readtree.jl\", sysimage_path=\"./unroot.so\", replace_default=false)'","category":"page"},{"location":"advanced/reduce_latency/","page":"Reduce startup latency","title":"Reduce startup latency","text":"profit:","category":"page"},{"location":"advanced/reduce_latency/","page":"Reduce startup latency","title":"Reduce startup latency","text":"> time julia -J ./unroot.so readtree.jl \nt[1, :Electron_dxy] = Float32[0.00037050247]\n\n________________________________________________________\nExecuted in 619.20 millis fish external\n usr time 902.29 millis 0.00 millis 902.29 millis\n sys time 658.59 millis 1.05 millis 657.54 millis","category":"page"},{"location":"#Introduction","page":"Introduction","title":"Introduction","text":"","category":"section"},{"location":"","page":"Introduction","title":"Introduction","text":"Apart from the pursue of performance, we also strive to provide intuitive and compostable interface. After all, \"theoretically\" fast doesn't mean the performance is accessible for the first-time physics user.","category":"page"},{"location":"#Status","page":"Introduction","title":"Status","text":"","category":"section"},{"location":"","page":"Introduction","title":"Introduction","text":"We support reading all scalar and jagged branches of \"basic\" types, provide indexing and iteration interface with a \"per branch\" basket-cache. There is a low level API to provide interpretation functionalities for custom types and classes. As a metric, UnROOT can read all branches (~1800) of CMS NanoAOD including jagged TLorentzVector branch.","category":"page"},{"location":"#Loops-aren't-slow","page":"Introduction","title":"Loops aren't slow","text":"","category":"section"},{"location":"","page":"Introduction","title":"Introduction","text":"One good thing about Julia is you can always fallback to writing loops since they are not intrinsically slower (than C/C++), certainly much faster than Python. Continuing the example from README:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> using UnROOT\n\njulia> f = ROOTFile(\"test/samples/NanoAODv5_sample.root\")\n\njulia> mytree = LazyTree(f, \"Events\", [\"Electron_dxy\", \"nMuon\", r\"Muon_(pt|eta)$\"])","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"There are essentially two loops you can use:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> for event in mytree\n ...\n end\n\njulia> for (i, event) in enumerate(mytree)\n # i will be index of `mytree`: 1, 2, 3...\n ...\n end","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"Both of which are compostable with @threads for multi-threading:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> Threads.@threads for event in mytree\n ...\n end\n\njulia> Threads.@threads for (i, event) in enumerate(mytree)\n ...\n end","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"Only one basket per branch will be cached so you don't have to worry about running out of RAM. At the same time, event inside the for-loop is not materialized until a field is accessed.","category":"page"},{"location":"#Laziness-in-Indexing,-Slicing,-and-Looping","page":"Introduction","title":"Laziness in Indexing, Slicing, and Looping","text":"","category":"section"},{"location":"","page":"Introduction","title":"Introduction","text":"Laziness (or eagerness) in UnROOT generally refers to if an \"event\" has read each branches of the tree or not. As canonical example of eager event, consider indexing:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> const r = LazyTree(ROOTFile(\"./Run2012BC_DoubleMuParked_Muons.root\"), \"Events\", [\"nMuon\", \"Muon_phi\"]);\n\njulia> names(r)\n2-element Vector{String}:\n \"Muon_phi\"\n \"nMuon\"\n\njulia> r[1]\n(Muon_phi = Float32[-0.034272723, 2.5426154], nMuon = 0x00000002)","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"Where the iterate() over tree is lazy:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> const r = LazyTree(ROOTFile(\"./Run2012BC_DoubleMuParked_Muons.root\"), \"Events\", [\"nMuon\", \"Muon_phi\"]);\n\njulia> for (i, evt) in enumerate(r)\n @show i, evt\n break\n end\n(i, evt) = (1, \"LazyEvent with: (:tree, :idx)\")","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"And the reading of actual data is delayed until evt.nMuon or evt.Muon_phi happens. Which means you should be careful about: Don't-\"double-access\".","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"The laziness of the main interfaces are summarized below:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":" mytree enumerate(mytree)\nfor X in ... 💤 💤\n@threads for X in ... 💤 💤\ngetindex(tree, row::Int) 💤 N/A\ngetindex(tree, row::Range) 🚨 N/A","category":"page"},{"location":"#Lazy-tree-construction","page":"Introduction","title":"Lazy tree construction","text":"","category":"section"},{"location":"","page":"Introduction","title":"Introduction","text":"As seen in the previous section, LazyTrees are cheap and offer a convenient way to create an object that isolates the branches of interest. It's fairly common that multiple branches are present with slightly differring names, like pos.x, pos.y etc. The LazyTree function also takes regular expressions, as seen in the example below where r\"Evt/trks/trks.pos.[xyz]\" is passed, that will match the corresponding branches:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> f = UnROOT.samplefile(\"km3net_offline.root\")\nROOTFile with 2 entries and 25 streamers.\n/Users/tamasgal/Dev/UnROOT.jl/test/samples/km3net_offline.root\n├─ E (TTree)\n│ └─ \"Evt\"\n└─ Header (Head)\n\njulia> t = LazyTree(f, \"E\", [\"Evt/trks/trks.id\", r\"Evt/trks/trks.pos.[xyz]\"])\n Row │ Evt_trks_trks_i Evt_trks_trks_p Evt_trks_trks_p Evt_trks_trks_p ⋯\n │ SubArray{Int32, SubArray{Float6 SubArray{Float6 SubArray{Float6 ⋯\n─────┼───────────────────────────────────────────────────────────────────────────\n 1 │ [1, 2, 3, 4, 5, [615.0, 615.0, [446.0, 446.0, [125.0, 125.0, 70.7, ⋯\n 2 │ [1, 2, 3, 4, 5, [533.0, 533.0, [465.0, 465.0, [80.7, 80.7, 39.1, 3 ⋯\n 3 │ [1, 2, 3, 4, 5, [593.0, 593.0, [457.0, 457.0, [194.0, 194.0, 96.5, ⋯\n 4 │ [1, 2, 3, 4, 5, [590.0, 590.0, [440.0, 440.0, [204.0, 204.0, 124.0 ⋯\n 5 │ [1, 2, 3, 4, 5, [546.0, 546.0, [440.0, 440.0, [58.6, 58.6, 30.1, 3 ⋯\n 6 │ [1, 2, 3, 4, 5, [585.0, 585.0, [424.0, 424.0, [202.0, 202.0, 183.0 ⋯\n 7 │ [1, 2, 3, 4, 5, [533.0, 533.0, [440.0, 440.0, [47.3, 47.3, 30.1, 2 ⋯\n 8 │ [1, 2, 3, 4, 5, [569.0, 569.0, [469.0, 469.0, [200.0, 200.0, 179.0 ⋯\n 9 │ [1, 2, 3, 4, 5, [557.0, 557.0, [412.0, 412.0, [209.0, 209.0, 101.0 ⋯\n 10 │ [1, 2, 3, 4, 5, [532.0, 532.0, [443.0, 443.0, [172.0, 172.0, 126.0 ⋯\n 1 column omitted\n\njulia> names(t)\n4-element Vector{String}:\n \"Evt_trks_trks_id\"\n \"Evt_trks_trks_pos_y\"\n \"Evt_trks_trks_pos_x\"\n \"Evt_trks_trks_pos_z\"\n\njulia> t.Evt_trks_trks_pos_y\n10-element LazyBranch{SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true},\nUnROOT.Nooffsetjagg, ArraysOfArrays.VectorOfVectors{Float64, Vector{Float64}, Vector{Int32},\nVector{Tuple{}}}}:\n [615.1089636184813, 615.1089636184813, … 574.836340445788, 576.5382993955498]\n ...\n ...","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"Branch names are normalised so that they contain valid characters for identifiers. The branchname Evt/trks/trks.pos.y for example is therefore converted to Evt_trks_trks_posy, which might be a bit inconvenient to use. LazyTree can rename branches based on regular expressions and subsitution strings (in Julia these are created with s\"\") which can be passed as Pairs. The example below shows how to use this:","category":"page"},{"location":"","page":"Introduction","title":"Introduction","text":"julia> t = LazyTree(f, \"E\", [r\"Evt/trks/trks.(dir|pos).([xyz])\" => s\"\\1_\\2\"])\n Row │ pos_z dir_z pos_y dir_y ⋯\n │ SubArray{Float6 SubArray{Float6 SubArray{Float6 SubArray{Float6 ⋯\n─────┼─────────────────────────────────────────────────────────────────────────────────────\n 1 │ [125.0, 125.0, 70.7 [-0.873, -0.873, -0 [615.0, 615.0, 585. [-0.487, -0.487, -0 ⋯\n 2 │ [80.7, 80.7, 39.1, [-0.835, -0.835, -0 [533.0, 533.0, 559. [0.521, 0.521, 0.52 ⋯\n 3 │ [194.0, 194.0, 96.5 [-0.989, -0.989, -0 [593.0, 593.0, 581. [-0.122, -0.122, -0 ⋯\n 4 │ [204.0, 204.0, 124. [-0.968, -0.968, -0 [590.0, 590.0, 571. [-0.23, -0.23, -0.2 ⋯\n 5 │ [58.6, 58.6, 30.1, [-0.821, -0.821, -0 [546.0, 546.0, 565. [0.54, 0.54, 0.54, ⋯\n 2 columns omitted\n\njulia> names(t)\n6-element Vector{String}:\n \"pos_z\"\n \"dir_z\"\n \"pos_y\"\n \"dir_y\"\n \"dir_x\"\n \"pos_x\"","category":"page"},{"location":"devdocs/#Related-Projects","page":"For Contributors","title":"Related Projects","text":"","category":"section"},{"location":"devdocs/","page":"For Contributors","title":"For Contributors","text":"While the ROOT documentation does not contain a detailed description of the binary structure, the format can be triangulated by other packages like","category":"page"},{"location":"devdocs/","page":"For Contributors","title":"For Contributors","text":"uproot3 (Python), see also UpROOT.jl\ngroot (Go)\nroot-io (Rust)\nLaurelin (Java)","category":"page"},{"location":"devdocs/","page":"For Contributors","title":"For Contributors","text":"Here's a detailed from-scratch walk through on reading a jagged branch from a ROOT file, recommended for first time contributors or those who just want to learn about ROOT file format.","category":"page"},{"location":"devdocs/","page":"For Contributors","title":"For Contributors","text":"Three's also a discussion reagarding the ROOT binary format documentation on uproot's issue page.","category":"page"}] +} diff --git a/previews/PR276/siteinfo.js b/previews/PR276/siteinfo.js new file mode 100644 index 00000000..612c9d46 --- /dev/null +++ b/previews/PR276/siteinfo.js @@ -0,0 +1 @@ +var DOCUMENTER_CURRENT_VERSION = "previews/PR276";