From 3613286dfd0d208991dbcb0a26722eb2247ff6a8 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Wed, 27 Mar 2024 08:10:42 +0000 Subject: [PATCH] build based on 0c4bbea --- dev/.documenter-siteinfo.json | 2 +- dev/assets/documenter.js | 923 +++++++++++++++----------- dev/assets/themes/documenter-dark.css | 2 +- dev/basicReconstruction.html | 2 +- dev/datasetStore.html | 2 +- dev/index.html | 2 +- dev/matrixCompression.html | 2 +- dev/multiContrast.html | 2 +- dev/multiPatch.html | 2 +- dev/objects.inv | Bin 0 -> 610 bytes dev/overview.html | 2 +- dev/parameters.html | 2 +- dev/recoResults.html | 2 +- 13 files changed, 553 insertions(+), 392 deletions(-) create mode 100644 dev/objects.inv diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 56ce523..d5ce7ea 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-02-10T08:25:44","documenter_version":"1.2.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-27T08:10:39","documenter_version":"1.3.0"}} \ No newline at end of file diff --git a/dev/assets/documenter.js b/dev/assets/documenter.js index f531160..c6562b5 100644 --- a/dev/assets/documenter.js +++ b/dev/assets/documenter.js @@ -4,7 +4,6 @@ requirejs.config({ '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', @@ -103,9 +102,10 @@ $(document).on("click", ".docstring header", function () { }); }); -$(document).on("click", ".docs-article-toggle-button", function () { +$(document).on("click", ".docs-article-toggle-button", function (event) { let articleToggleTitle = "Expand docstring"; let navArticleToggleTitle = "Expand all docstrings"; + let animationSpeed = event.noToggleAnimation ? 0 : 400; debounce(() => { if (isExpanded) { @@ -116,7 +116,7 @@ $(document).on("click", ".docs-article-toggle-button", function () { isExpanded = false; - $(".docstring section").slideUp(); + $(".docstring section").slideUp(animationSpeed); } else { $(this).removeClass("fa-chevron-down").addClass("fa-chevron-up"); $(".docstring-article-toggle-button") @@ -127,7 +127,7 @@ $(document).on("click", ".docs-article-toggle-button", function () { articleToggleTitle = "Collapse docstring"; navArticleToggleTitle = "Collapse all docstrings"; - $(".docstring section").slideDown(); + $(".docstring section").slideDown(animationSpeed); } $(this).prop("title", navArticleToggleTitle); @@ -224,224 +224,465 @@ $(document).ready(function () { }) //////////////////////////////////////////////////////////////////////////////// -require(['jquery', 'minisearch'], function($, 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 +require(['jquery'], function($) { -let results = []; -let timer = undefined; +$(document).ready(function () { + let meta = $("div[data-docstringscollapsed]").data(); -let data = documenterSearchIndex["docs"].map((x, key) => { - x["id"] = key; // minisearch requires a unique for each object - return x; + if (meta?.docstringscollapsed) { + $("#documenter-article-toggle-button").trigger({ + type: "click", + noToggleAnimation: true, + }); + } }); -// list below is the lunr 2.1.3 list minus the intersect with names(Base) -// (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with) -// ideally we'd just filter the original list but it's not available as a variable -const stopWords = new Set([ - "a", - "able", - "about", - "across", - "after", - "almost", - "also", - "am", - "among", - "an", - "and", - "are", - "as", - "at", - "be", - "because", - "been", - "but", - "by", - "can", - "cannot", - "could", - "dear", - "did", - "does", - "either", - "ever", - "every", - "from", - "got", - "had", - "has", - "have", - "he", - "her", - "hers", - "him", - "his", - "how", - "however", - "i", - "if", - "into", - "it", - "its", - "just", - "least", - "like", - "likely", - "may", - "me", - "might", - "most", - "must", - "my", - "neither", - "no", - "nor", - "not", - "of", - "off", - "often", - "on", - "or", - "other", - "our", - "own", - "rather", - "said", - "say", - "says", - "she", - "should", - "since", - "so", - "some", - "than", - "that", - "the", - "their", - "them", - "then", - "there", - "these", - "they", - "this", - "tis", - "to", - "too", - "twas", - "us", - "wants", - "was", - "we", - "were", - "what", - "when", - "who", - "whom", - "why", - "will", - "would", - "yet", - "you", - "your", -]); - -let index = new minisearch({ - fields: ["title", "text"], // fields to index for full-text search - storeFields: ["location", "title", "text", "category", "page"], // fields to return with search results - processTerm: (term) => { - let word = stopWords.has(term) ? null : term; - if (word) { - // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names - word = word - .replace(/^[^a-zA-Z0-9@!]+/, "") - .replace(/[^a-zA-Z0-9@!]+$/, ""); - } +}) +//////////////////////////////////////////////////////////////////////////////// +require(['jquery'], function($) { - 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, +/* +To get an in-depth about the thought process you can refer: https://hetarth02.hashnode.dev/series/gsoc + +PSEUDOCODE: + +Searching happens automatically as the user types or adjusts the selected filters. +To preserve responsiveness, as much as possible of the slow parts of the search are done +in a web worker. Searching and result generation are done in the worker, and filtering and +DOM updates are done in the main thread. The filters are in the main thread as they should +be very quick to apply. This lets filters be changed without re-searching with minisearch +(which is possible even if filtering is on the worker thread) and also lets filters be +changed _while_ the worker is searching and without message passing (neither of which are +possible if filtering is on the worker thread) + +SEARCH WORKER: + +Import minisearch + +Build index + +On message from main thread + run search + find the first 200 unique results from each category, and compute their divs for display + note that this is necessary and sufficient information for the main thread to find the + first 200 unique results from any given filter set + post results to main thread + +MAIN: + +Launch worker + +Declare nonconstant globals (worker_is_running, last_search_text, unfiltered_results) + +On text update + if worker is not running, launch_search() + +launch_search + set worker_is_running to true, set last_search_text to the search text + post the search query to worker + +on message from worker + if last_search_text is not the same as the text in the search field, + the latest search result is not reflective of the latest search query, so update again + launch_search() + otherwise + set worker_is_running to false + + regardless, display the new search results to the user + save the unfiltered_results as a global + update_search() + +on filter click + adjust the filter selection + update_search() + +update_search + apply search filters by looping through the unfiltered_results and finding the first 200 + unique results that match the filters + + Update the DOM +*/ + +/////// SEARCH WORKER /////// + +function worker_function(documenterSearchIndex, documenterBaseURL, filters) { + importScripts( + "https://cdn.jsdelivr.net/npm/minisearch@6.1.0/dist/umd/index.min.js" + ); + + let data = documenterSearchIndex.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 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@!]+$/, ""); + + word = word.toLowerCase(); } 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: { + prefix: true, + boost: { title: 100 }, + fuzzy: 2, + }, + }); -index.addAll(data); + index.addAll(data); + + /** + * Used to map characters to HTML entities. + * Refer: https://github.com/lodash/lodash/blob/main/src/escape.ts + */ + const htmlEscapes = { + "&": "&", + "<": "<", + ">": ">", + '"': """, + "'": "'", + }; + + /** + * Used to match HTML entities and HTML characters. + * Refer: https://github.com/lodash/lodash/blob/main/src/escape.ts + */ + const reUnescapedHtml = /[&<>"']/g; + const reHasUnescapedHtml = RegExp(reUnescapedHtml.source); + + /** + * Escape function from lodash + * Refer: https://github.com/lodash/lodash/blob/main/src/escape.ts + */ + function escape(string) { + return string && reHasUnescapedHtml.test(string) + ? string.replace(reUnescapedHtml, (chr) => htmlEscapes[chr]) + : string || ""; + } -let filters = [...new Set(data.map((x) => x.category))]; -var modal_filters = make_modal_body_filters(filters); -var filter_results = []; + /** + * 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 += ` (${result.page})`; + } -$(document).on("keyup", ".documenter-search-input", function (event) { - // Adding a debounce to prevent disruptions from super-speed typing! - debounce(() => update_search(filter_results), 300); + let textindex = new RegExp(`${querystring}`, "i").exec(result.text); + let text = + textindex !== null + ? result.text.slice( + Math.max(textindex.index - 100, 0), + Math.min( + textindex.index + querystring.length + 100, + result.text.length + ) + ) + : ""; // cut-off text before and after from the match + + text = text.length ? escape(text) : ""; + + let display_result = text.length + ? "..." + + text.replace( + new RegExp(`${escape(querystring)}`, "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 = ` + +
+
${escape(result.title)}
+
${result.category}
+
+

+ ${display_result} +

+
+ ${display_link} +
+ + ${search_divider} + `; + + return result_div; + } + + self.onmessage = function (e) { + let query = e.data; + let results = index.search(query, { + filter: (result) => { + // Only return relevant results + return result.score >= 1; + }, + }); + + // Pre-filter to deduplicate and limit to 200 per category to the extent + // possible without knowing what the filters are. + let filtered_results = []; + let counts = {}; + for (let filter of filters) { + counts[filter] = 0; + } + let present = {}; + + for (let result of results) { + cat = result.category; + cnt = counts[cat]; + if (cnt < 200) { + id = cat + "---" + result.location; + if (present[id]) { + continue; + } + present[id] = true; + filtered_results.push({ + location: result.location, + category: cat, + div: make_search_result(result, query), + }); + } + } + + postMessage(filtered_results); + }; +} + +// `worker = Threads.@spawn worker_function(documenterSearchIndex)`, but in JavaScript! +const filters = [ + ...new Set(documenterSearchIndex["docs"].map((x) => x.category)), +]; +const worker_str = + "(" + + worker_function.toString() + + ")(" + + JSON.stringify(documenterSearchIndex["docs"]) + + "," + + JSON.stringify(documenterBaseURL) + + "," + + JSON.stringify(filters) + + ")"; +const worker_blob = new Blob([worker_str], { type: "text/javascript" }); +const worker = new Worker(URL.createObjectURL(worker_blob)); + +/////// SEARCH MAIN /////// + +// Whether the worker is currently handling a search. This is a boolean +// as the worker only ever handles 1 or 0 searches at a time. +var worker_is_running = false; + +// The last search text that was sent to the worker. This is used to determine +// if the worker should be launched again when it reports back results. +var last_search_text = ""; + +// The results of the last search. This, in combination with the state of the filters +// in the DOM, is used compute the results to display on calls to update_search. +var unfiltered_results = []; + +// Which filter is currently selected +var selected_filter = ""; + +$(document).on("input", ".documenter-search-input", function (event) { + if (!worker_is_running) { + launch_search(); + } }); +function launch_search() { + worker_is_running = true; + last_search_text = $(".documenter-search-input").val(); + worker.postMessage(last_search_text); +} + +worker.onmessage = function (e) { + if (last_search_text !== $(".documenter-search-input").val()) { + launch_search(); + } else { + worker_is_running = false; + } + + unfiltered_results = e.data; + update_search(); +}; + $(document).on("click", ".search-filter", function () { if ($(this).hasClass("search-filter-selected")) { - $(this).removeClass("search-filter-selected"); + selected_filter = ""; } else { - $(this).addClass("search-filter-selected"); + selected_filter = $(this).text().toLowerCase(); } - // Adding a debounce to prevent disruptions from crazy clicking! - debounce(() => get_filters(), 300); + // This updates search results and toggles classes for UI: + update_search(); }); -/** - * 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!
- `; - +function update_search() { 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) - ); - } - }, - }); + if (selected_filter == "") { + results = unfiltered_results; + } else { + results = unfiltered_results.filter((result) => { + return selected_filter == result.category.toLowerCase(); + }); + } let search_result_container = ``; + let modal_filters = make_modal_body_filters(); let search_divider = `
`; if (results.length) { @@ -449,19 +690,23 @@ function update_search(selected_filters = []) { 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++; - } - + for (var i = 0, n = results.length; i < n && count < 200; ++i) { + let result = results[i]; + if (result.location && !links.includes(result.location)) { + search_results += result.div; + count++; links.push(result.location); } - }); + } - let result_count = `
${count} result(s)
`; + if (count == 1) { + count_str = "1 result"; + } else if (count == 200) { + count_str = "200+ results"; + } else { + count_str = count + " results"; + } + let result_count = `
${count_str}
`; search_result_container = `
@@ -490,125 +735,37 @@ function update_search(selected_filters = []) { $(".search-modal-card-body").html(search_result_container); } else { - filter_results = []; - modal_filters = make_modal_body_filters(filters, filter_results); - if (!$(".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); + $(".search-modal-card-body").html(` +
Type something to get started!
+ `); } } /** * Make the modal filter html * - * @param {string[]} filters - * @param {string[]} selected_filters * @returns string */ -function make_modal_body_filters(filters, selected_filters = []) { - let str = ``; - - filters.forEach((val) => { - if (selected_filters.includes(val)) { - str += `${val}`; - } else { - str += `${val}`; - } - }); +function make_modal_body_filters() { + let str = filters + .map((val) => { + if (selected_filter == val.toLowerCase()) { + return `${val}`; + } else { + return `${val}`; + } + }) + .join(""); - let filter_html = ` + return `
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); +
`; } }) @@ -635,103 +792,107 @@ $(document).ready(function () { //////////////////////////////////////////////////////////////////////////////// require(['jquery'], function($) { -let search_modal_header = ` -
-
-

- - - - -

-
-
- -
-
-`; - -let initial_search_body = ` -
Type something to get started!
-`; - -let search_modal_footer = ` - -`; - -$(document.body).append( - ` - + weights=nothing, kargs...)

One can see that it requires the system matrix S and the measurements u to be already loaded.

We note that S is typeless for a reason here. For a regular reconstruction one will basically feed in an Array{ComplexF32,2} in here, although more precisely it will be a Transposed version of that type if the Kaczmarz algorithm is being used for efficiency reasons.

However, in case that matrix compression is applied S will be of type SparseMatrixCSC. And for Multi-Patch Reconstruction S will be of type MultiPatchOperator. Hence, the solvers are implemented in a very generic way and require only certain functions to be implemented. The low level reconstruction method calls one of the solvers from RegularizedLeastSquares.jl.

diff --git a/dev/datasetStore.html b/dev/datasetStore.html index 660f5c1..427f50a 100644 --- a/dev/datasetStore.html +++ b/dev/datasetStore.html @@ -1,2 +1,2 @@ -- · MPI Reconstruction
GitHub

Layers

The reconstruction function has several layers starting from a high level over several middle layer to low layer functions. The most high level method has the following signature `$julia reconstruction(d::MDFDatasetStore, study::Study, exp::Experiment, recoParams::Dict{String,Any})$

+- · MPI Reconstruction
GitHub

Layers

The reconstruction function has several layers starting from a high level over several middle layer to low layer functions. The most high level method has the following signature `$julia reconstruction(d::MDFDatasetStore, study::Study, exp::Experiment, recoParams::Dict{String,Any})$

diff --git a/dev/index.html b/dev/index.html index 4b88350..c0983c4 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · MPI Reconstruction
GitHub

MPIReco.jl

Julia package for the reconstruction of magnetic particle imaging (MPI) data

Introduction

This project provides functions for the reconstruction of MPI data. The project is implemented in the programming language Julia and contains algorithms for

Key features are

  • Frequency filtering for memory efficient reconstruction. Only frequencies used during reconstructions are loaded into memory.
  • Different solvers provided by the package RegularizedLeastSquares.jl
  • High-level until low-level reconstruction providing maximum flexibility for the user
  • Spectral leakage correction (implemented in MPIFiles.jl)

Installation

Start julia and open the package mode by entering ]. Then enter

add MPIReco

This will install the packages MPIReco.jl and all its dependencies. In particular this will install the core dependencies MPIFiles and RegularizedLeastSquares.

License / Terms of Usage

The source code of this project is licensed under the MIT license. This implies that you are free to use, share, and adapt it. However, please give appropriate credit by citing the project.

Contact

If you have problems using the software, find mistakes, or have general questions please use the issue tracker to contact us.

Contributors

+Home · MPI Reconstruction
GitHub

MPIReco.jl

Julia package for the reconstruction of magnetic particle imaging (MPI) data

Introduction

This project provides functions for the reconstruction of MPI data. The project is implemented in the programming language Julia and contains algorithms for

Key features are

  • Frequency filtering for memory efficient reconstruction. Only frequencies used during reconstructions are loaded into memory.
  • Different solvers provided by the package RegularizedLeastSquares.jl
  • High-level until low-level reconstruction providing maximum flexibility for the user
  • Spectral leakage correction (implemented in MPIFiles.jl)

Installation

Start julia and open the package mode by entering ]. Then enter

add MPIReco

This will install the packages MPIReco.jl and all its dependencies. In particular this will install the core dependencies MPIFiles and RegularizedLeastSquares.

License / Terms of Usage

The source code of this project is licensed under the MIT license. This implies that you are free to use, share, and adapt it. However, please give appropriate credit by citing the project.

Contact

If you have problems using the software, find mistakes, or have general questions please use the issue tracker to contact us.

Contributors

diff --git a/dev/matrixCompression.html b/dev/matrixCompression.html index 3f0ca7f..3b48480 100644 --- a/dev/matrixCompression.html +++ b/dev/matrixCompression.html @@ -1,2 +1,2 @@ -Compression · MPI Reconstruction
GitHub

Matrix-Compression Techniques

The reconstruction can be accelerated by applying matrix compression. To this end, the system matrix S is transformed into a different domain by applying a basis transformation on the rows of the system matrix. In MPIReco.jl, matrix compression can be enabled by specifying sparseTrafo which can be "DCT-IV" or "FFT".

The transformations can be restricted to the drive-field field-of-view by setting useDFFoV = true. The compression factor that controls how many coefficients are dropped after application of the transformation is controlled by the parameter redFactor. For instance a reduction factor of redFactor = 0.01 will drop 99 % of the data.

+Compression · MPI Reconstruction
GitHub

Matrix-Compression Techniques

The reconstruction can be accelerated by applying matrix compression. To this end, the system matrix S is transformed into a different domain by applying a basis transformation on the rows of the system matrix. In MPIReco.jl, matrix compression can be enabled by specifying sparseTrafo which can be "DCT-IV" or "FFT".

The transformations can be restricted to the drive-field field-of-view by setting useDFFoV = true. The compression factor that controls how many coefficients are dropped after application of the transformation is controlled by the parameter redFactor. For instance a reduction factor of redFactor = 0.01 will drop 99 % of the data.

diff --git a/dev/multiContrast.html b/dev/multiContrast.html index bc9dc5a..1b03b1f 100644 --- a/dev/multiContrast.html +++ b/dev/multiContrast.html @@ -2,4 +2,4 @@ Multi-Contrast · MPI Reconstruction
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Multi-Contrast Reconstruction

Until now we have discussed single-contrast reconstruction in which case the reconstructed image c has a singleton first dimension. To perform multi-contrast reconstruction one has to specify multiple system matrices

bSFa = MPIFile(filenameA)
 bSFb = MPIFile(filenameB)

and can then invoke

c = reconstruction([bSFa, bSFb], b;
                     SNRThresh=5, frames=1, minFreq=80e3,
-                    recChannels=1:2, iterations=1)

Now one can access the first and second channel by c[1,:,:,:] and c[2,:,:,:].

+ recChannels=1:2, iterations=1)

Now one can access the first and second channel by c[1,:,:,:] and c[2,:,:,:].

diff --git a/dev/multiPatch.html b/dev/multiPatch.html index 309c07b..264eeda 100644 --- a/dev/multiPatch.html +++ b/dev/multiPatch.html @@ -18,4 +18,4 @@ c4 = reconstruction(bSFs, b; SNRThresh=5, frames=1, minFreq=80e3, recChannels=1:2,iterations=1, spectralLeakageCorrection=false, mapping=mapping, systemMatrices = S, SFGridCenter=SFGridCenter, - FFPos=FFPos, FFPosSF=FFPos) + FFPos=FFPos, FFPosSF=FFPos) diff --git a/dev/objects.inv b/dev/objects.inv new file mode 100644 index 0000000000000000000000000000000000000000..802c0e73ca5c609675bb6b71a08ea039390d71b5 GIT binary patch literal 610 zcmV-o0-gOMAX9K?X>NERX>N99Zgg*Qc_4OWa&u{KZXhxWBOp+6Z)#;@bUGkSP)Q(C zWn*t{b98cbV{~b6ZVDqHR%LQ?X>V>iATTa9E;0%uAXI2&AaZ4GVQFq;WpW^IW*~HE zX>%ZEX>4U6X>%ZBZ*6dLWpi_7WFU2OX>MmAdTeQ8E(&;@rIg!F<1i40@BI{(cK6aC zxa1NLOQl9su=@aRGNlH`X65O{QZt+eveQMd{B$cRikUlE~xN< zvpu$w-s={KK7u(4cu)8AvAFFwAPV(NpO71bhHSYN^&`|;Su}?lg;ps%la4yqK0)&g zdE!&{t@g!Vn!t4h;$3my05s=3JtfI5?LZLl@GB#7SRpIdOzVp zG=)Ndv>c82xY6yK0c(rGOp=jL0%Wb<*&2=@*-U*U--2AK@QgW{Hm-TJM$kcYxwA=bwPT?nHx*8YFpQi}fs? zrq>CSS62Gz~)KaB^D3x&5^AvxnEXXxNov6|~xXp6acYqETRC w+-&}RU+Qdn4%HrpZK1x&NBtmG4Eyem7P*xC+t(Wo6WfFHy

Lets go through that script step by step. First, we create handles for the system matrix and the measurement data. Both are of the type MPIFile which is an abstract type that can for instance be an MDFFile or a BrukerFile.

Using the handles to the MPI datasets we can call the reconstruction function that has various variants depending on the types that are passed to it. Here, we exploit the multiple dispatch mechanism of julia. In addition to the file handles we also apply several reconstruction parameters using keyword arguments. In this case, we set the SNR threshold to 5 implying that only matrix rows with an SNR above 5 are used during reconstruction. The parameter frame decides which frame of the measured data should be reconstructed.

The object c is of type ImageMeta and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. More details on the return type are discussed in the Reconstruction Results

Data Storage

One can store the reconstruction result into an MDF file by calling

saveRecoData("filename.mdf", c)

In order to load the data one calls

c = loadRecoData("filename.mdf", c)

We will next take a closer look at different forms of the reconstruction routine.

+

Lets go through that script step by step. First, we create handles for the system matrix and the measurement data. Both are of the type MPIFile which is an abstract type that can for instance be an MDFFile or a BrukerFile.

Using the handles to the MPI datasets we can call the reconstruction function that has various variants depending on the types that are passed to it. Here, we exploit the multiple dispatch mechanism of julia. In addition to the file handles we also apply several reconstruction parameters using keyword arguments. In this case, we set the SNR threshold to 5 implying that only matrix rows with an SNR above 5 are used during reconstruction. The parameter frame decides which frame of the measured data should be reconstructed.

The object c is of type ImageMeta and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. More details on the return type are discussed in the Reconstruction Results

Data Storage

One can store the reconstruction result into an MDF file by calling

saveRecoData("filename.mdf", c)

In order to load the data one calls

c = loadRecoData("filename.mdf", c)

We will next take a closer look at different forms of the reconstruction routine.

diff --git a/dev/parameters.html b/dev/parameters.html index 5fb3ca7..8e082bd 100644 --- a/dev/parameters.html +++ b/dev/parameters.html @@ -1,2 +1,2 @@ -Parameters · MPI Reconstruction
GitHub
+Parameters · MPI Reconstruction
GitHub
diff --git a/dev/recoResults.html b/dev/recoResults.html index f2a6d28..f0a407d 100644 --- a/dev/recoResults.html +++ b/dev/recoResults.html @@ -1,2 +1,2 @@ -Results · MPI Reconstruction
GitHub

Reconstruction Results

The object c is of type ImageMeta and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. c has in total 5 dimensions. The first dimension encodes multi-spectral channels. Dimensions 2-4 encode the three spatial dimensions. The last dimension contains the number of frames being stored in c.

+Results · MPI Reconstruction
GitHub

Reconstruction Results

The object c is of type ImageMeta and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. c has in total 5 dimensions. The first dimension encodes multi-spectral channels. Dimensions 2-4 encode the three spatial dimensions. The last dimension contains the number of frames being stored in c.