diff --git a/_static/basic.css b/_static/basic.css index 30fee9d..f316efc 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/classic.css b/_static/classic.css index 9ad992b..5530147 100644 --- a/_static/classic.css +++ b/_static/classic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- classic theme. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/doctools.js b/_static/doctools.js index d06a71d..4d67807 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -4,7 +4,7 @@ * * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/language_data.js b/_static/language_data.js index 250f566..367b8ed 100644 --- a/_static/language_data.js +++ b/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -13,7 +13,7 @@ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/_static/searchtools.js b/_static/searchtools.js index 7918c3f..92da3f8 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +137,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +176,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -239,16 +268,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,16 +304,32 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - results.push([ + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -308,46 +344,47 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +398,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -466,14 +508,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +542,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -549,8 +594,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/_static/sidebar.js b/_static/sidebar.js index c5e2692..f28c206 100644 --- a/_static/sidebar.js +++ b/_static/sidebar.js @@ -16,7 +16,7 @@ * Once the browser is closed the cookie is deleted and the position * reset to the default (expanded). * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/api.html b/api.html index 04faf63..00af5fa 100644 --- a/api.html +++ b/api.html @@ -7,10 +7,10 @@ API — tomojs-pytools documentation - + - + @@ -285,6 +285,21 @@

Navigation

+
+pytools.meta.is_16bit(file_path: str | Path) → bool
+

Read an image file header to inspect meta-data.

+

Supported file formats include TIFF, and others supported by SimpleITK and the Insight toolkit.

+
+
Parameters:
+

file_path – The path to an image file.

+
+
Returns:
+

True if the pixel type is a 16-bit integer (signed or unsigned), False otherwise.

+
+
+
+ +
pytools.meta.is_int16(file_path: str | Path) → bool

Read an image file header to inspect meta-data.

@@ -451,6 +466,7 @@

Table of Contents

  • visual_min_max()
  • zarr_extract_2d()
    • +
  • is_16bit()
  • is_int16()
  • bin_shrink()
  • build_pyramid()
    • @@ -478,7 +494,7 @@

    This Page

    rel="nofollow">Show Source - + @@ -510,7 +526,7 @@

    Navigation

    \ No newline at end of file diff --git a/commandline.html b/commandline.html index 0745ce6..4381dcb 100644 --- a/commandline.html +++ b/commandline.html @@ -7,10 +7,10 @@ Command Line Interface — tomojs-pytools documentation - + - + @@ -196,7 +196,7 @@

    This Page

    rel="nofollow">Show Source - + @@ -231,7 +231,7 @@

    Navigation

    \ No newline at end of file diff --git a/development.html b/development.html index 145ef0c..b16036e 100644 --- a/development.html +++ b/development.html @@ -7,10 +7,10 @@ Development — tomojs-pytools documentation - + - + @@ -205,7 +205,7 @@

    This Page

    rel="nofollow">Show Source - + @@ -240,7 +240,7 @@

    Navigation

    \ No newline at end of file diff --git a/genindex.html b/genindex.html index 9917995..4b2ac68 100644 --- a/genindex.html +++ b/genindex.html @@ -6,10 +6,10 @@ Index — tomojs-pytools documentation - + - + @@ -196,6 +196,8 @@

    I

    @@ -405,7 +407,7 @@

    Z

    @@ -434,7 +436,7 @@

    Navigation

    \ No newline at end of file diff --git a/index.html b/index.html index 0c09fd1..ac3dd6e 100644 --- a/index.html +++ b/index.html @@ -7,10 +7,10 @@ Welcome to pytools’s documentation! — tomojs-pytools documentation - + - + @@ -81,6 +81,7 @@

    InstallationHedwigZarrImages
  • visual_min_max()
  • zarr_extract_2d()
    • +
  • is_16bit()
  • is_int16()
  • bin_shrink()
  • build_pyramid()
    • @@ -127,7 +128,7 @@

    This Page

    rel="nofollow">Show Source - + @@ -159,7 +160,7 @@

    Navigation

    \ No newline at end of file diff --git a/objects.inv b/objects.inv index dedc500..1443c71 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html index e1f1715..9249b50 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -6,10 +6,10 @@ Python Module Index — tomojs-pytools documentation - + - + @@ -93,7 +93,7 @@

    Python Module Index

    @@ -122,7 +122,7 @@

    Navigation

    \ No newline at end of file diff --git a/search.html b/search.html index f4adbbe..2fad6bd 100644 --- a/search.html +++ b/search.html @@ -6,19 +6,20 @@ Search — tomojs-pytools documentation - + - + - - + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js index c78e065..422db8a 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api", "commandline", "development", "index"], "filenames": ["api.rst", "commandline.rst", "development.rst", "index.rst"], "titles": ["API", "Command Line Interface", "Development", "Welcome to pytools\u2019s documentation!"], "terms": {"class": 0, "pytool": [0, 1, 2], "hedwigzarrimag": [0, 3], "zarr_grp": 0, "group": 0, "_ome_info": 0, "omeinfo": 0, "_ome_idx": 0, "int": 0, "none": 0, "repres": 0, "om": 0, "ngff": 0, "zarr": [0, 1], "pyramid": 0, "imag": [0, 1, 2, 3], "The": [0, 1, 2, 3], "member": [0, 2], "provid": [0, 2, 3], "inform": 0, "us": [0, 1, 2, 3], "hedwig": [0, 3], "pipelin": 0, "properti": 0, "dim": 0, "str": 0, "dimens": [0, 1], "xy": 0, "xyc": 0, "xyzct": 0, "etc": 0, "collaps": 0, "zct": 0, "size": [0, 1], "1": [0, 2], "note": [0, 3], "thi": [0, 2, 3], "i": [0, 2, 3], "revers": 0, "order": [0, 3], "axi": 0, "numpi": 0, "dask": 0, "extract_2d": 0, "target_size_x": 0, "target_size_i": 0, "size_factor": 0, "float": 0, "5": 0, "auto_uint8": 0, "bool": 0, "fals": [0, 1], "extract": 0, "2d": 0, "simpleitk": [0, 1], "from": [0, 2, 3], "an": [0, 1, 3], "structur": 0, "arrai": 0, "like": 0, "assum": 0, "have": [0, 2], "follow": [0, 1, 2], "ax": 0, "spacial": 0, "must": [0, 2], "label": 0, "x": 0, "y": 0, "option": [0, 1, 2, 3], "z": 0, "If": 0, "space": 0, "exist": 0, "time": [0, 3], "channel": 0, "all": [0, 2], "ar": [0, 2, 3], "subvolum": 0, "resiz": 0, "target": 0, "while": 0, "maintain": 0, "aspect": 0, "ratio": 0, "same": 0, "pixel": 0, "type": 0, "paramet": 0, "increas": 0, "factor": 0, "so": [0, 3], "can": [0, 1, 2, 3], "antialias": 0, "appli": 0, "true": 0, "output": 0, "automat": [0, 2], "linearli": 0, "shift": 0, "scale": 0, "fit": 0, "uint8": 0, "compon": [0, 2], "return": 0, "neuroglancer_shader_paramet": 0, "mad_scal": 0, "3": [0, 3], "middle_quantil": 0, "tupl": 0, "dict": 0, "produc": 0, "shaderparamet": 0, "portion": 0, "metadata": 0, "neuroglanc": 0, "determin": [0, 2], "which": [0, 2], "shader": 0, "render": [0, 2], "one": 0, "rgb": 0, "grayscal": 0, "multichannel": 0, "comput": 0, "full": 0, "resolut": [0, 1], "parallel": 0, "read": [0, 2], "statist": 0, "global": 0, "schedul": 0, "oper": [0, 2], "chang": [0, 2], "standard": 0, "configur": [0, 3], "For": [0, 2], "default": [0, 1, 2], "algorithm": 0, "rang": 0, "robust": 0, "median": 0, "absolut": 0, "deviat": 0, "mad": 0, "about": [0, 2], "minimum": 0, "maximum": 0, "quantil": 0, "data": [0, 2], "select": [0, 2], "visibl": 0, "intens": 0, "two": 0, "between": 0, "0": [0, 2], "first": 0, "valu": 0, "lower": 0, "second": 0, "upper": 0, "dictionari": 0, "suitabl": 0, "json": 0, "serial": 0, "ome_roi_model": 0, "iter": 0, "omeroimodel": 0, "get": [0, 2], "roi": 0, "model": [0, 2], "current": [0, 2, 3], "thei": [0, 1, 2, 3], "pars": 0, "xml": 0, "file": [0, 2], "gener": 0, "union": 0, "annot": 0, "rectangl": 0, "mai": 0, "empti": 0, "path": 0, "rechunk": 0, "chunk_siz": [0, 1], "compressor": [0, 1], "in_memori": 0, "chunk": [0, 1], "each": 0, "inplac": 0, "other": [0, 2], "ct": 0, "imagezarrimag": 0, "need": [0, 2, 3], "write": [0, 2], "access": 0, "integ": 0, "written": 0, "input": 0, "entir": 0, "load": 0, "memori": [0, 1], "uncompress": 0, "befor": [0, 2], "otherwis": 0, "directli": [0, 1], "former": 0, "faster": 0, "requir": [0, 1, 2, 3], "enough": 0, "hold": 0, "shader_typ": 0, "shape": 0, "unit": 0, "zarr_path": 0, "read_onli": 0, "set": [0, 2], "get_series_kei": 0, "string": 0, "name": 0, "Will": 0, "avail": [0, 1], "e": [0, 2], "g": 0, "label_imag": 0, "given": 0, "ome_info": 0, "anystr": 0, "ome_xml_path": 0, "seri": 0, "kei": 0, "store": [0, 1, 2], "visual_min_max": [0, 3], "input_imag": 0, "clamp": 0, "directori": [0, 2], "estim": 0, "visual": 0, "perform": 0, "io": [0, 3], "support": 0, "format": [0, 2], "mrc": 0, "mii": 0, "png": 0, "tiff": 0, "A": [0, 2], "detect": 0, "contain": [0, 1, 2, 3], "zarrai": 0, "subdirectori": 0, "commonli": 0, "Such": 0, "case": 0, "would": 0, "specifi": [0, 3], "dirnam": 0, "floor": 0, "limit": 0, "result": 0, "element": 0, "neuroglancerprecomputedmin": 0, "neuroglancerprecomputedmax": 0, "neuroglancerprecomputedfloor": 0, "neuroglancerprecomputedlimit": 0, "zarr_extract_2d": [0, 3], "input_zarr": [0, 1], "output_filenam": 0, "sampl": 0, "itk": 0, "imageio": 0, "place": [0, 2], "addit": 0, "jpeg": 0, "onli": [0, 2], "4": 0, "meta": 0, "is_int16": [0, 3], "file_path": 0, "header": 0, "inspect": 0, "includ": [0, 2, 3], "insight": 0, "toolkit": 0, "sign": 0, "16": 0, "bit": 0, "util": [0, 3], "bin_shrink": [0, 3], "img": 0, "shrink_dim": 0, "reduc": 0, "2": [0, 3], "xyz": 0, "averag": 0, "object": 0, "recommend": [0, 2], "fastest": 0, "slowest": 0, "build_pyramid": [0, 3], "list": 0, "shrink": 0, "overwrit": 0, "multipl": 0, "item": 0, "remain": 0, "histogram": 0, "daskhistogramhelp": [0, 3], "arr": 0, "modul": [0, 1, 2], "opt": 0, "hostedtoolcach": 0, "python": [0, 1, 2, 3], "9": 0, "19": 0, "x64": 0, "lib": 0, "python3": [0, 3], "site": 0, "packag": [0, 1, 2, 3], "__init__": 0, "py": [0, 3], "histogrambas": [0, 3], "zarrhistogramhelp": [0, 3], "filenam": 0, "histogram_robust_stat": [0, 3], "hist": 0, "bin_edg": 0, "weight": 0, "densiti": 0, "count": 0, "edg": 0, "bin": [0, 2], "should": [0, 2], "greater": 0, "than": 0, "histogram_stat": [0, 3], "mean": 0, "var": 0, "varianc": 0, "sigma": 0, "weighted_quantil": [0, 3], "sample_weight": 0, "values_sort": 0, "old_styl": 0, "veri": 0, "close": 0, "percentil": 0, "mani": [0, 2], "length": 0, "avoid": 0, "sort": 0, "initi": [0, 2], "correct": 0, "consist": 0, "convert": 0, "file_to_uint8": [0, 3], "in_file_path": 0, "out_file_path": 0, "255": 0, "unsign": 0, "8": 0, "sourc": [0, 2], "extens": 0, "differ": 0, "input_file_path": 0, "convers": 0, "uint16": 0, "done": 0, "point": [0, 1], "truncat": 0, "round": 0, "consid": 0, "implement": 0, "detail": [0, 2], "execut": [1, 2, 3], "variou": 1, "task": 1, "invok": 1, "help": 1, "Or": 1, "prefer": 1, "wai": 1, "entri": 1, "m": [1, 2, 3], "With": 1, "either": 1, "method": [1, 2], "section": [1, 2], "describ": 1, "sub": 1, "log": [1, 2], "level": 1, "log_level": 1, "debug": [1, 2], "info": 1, "warn": 1, "error": 1, "spatial": 1, "64": 1, "recompress": 1, "when": [1, 2], "version": [1, 3], "show": 1, "exit": [1, 3], "argument": [1, 3], "function": 1, "displai": 1, "1024x1024": 1, "doc": 2, "relat": 2, "pleas": 2, "clone": 2, "repositori": [2, 3], "locat": 2, "niaid": [2, 3], "enterpris": 2, "organ": 2, "account": 2, "larg": 2, "storag": 2, "larger": 2, "train": 2, "text": 2, "base": [2, 3], "code": 2, "instal": 2, "system": 2, "up": 2, "user": 2, "tool": 2, "": 2, "usag": 2, "duplic": 2, "here": [2, 3], "onc": 2, "usual": 2, "transpar": 2, "ad": 2, "branch": 2, "gitattribut": 2, "creat": 2, "virtual": 2, "environ": 2, "project": [2, 3], "venv": 2, "pkg": 2, "activ": 2, "pip": [2, 3], "r": 2, "dev": 2, "txt": [2, 3], "edit": 2, "mode": 2, "integr": 2, "them": 2, "driver": 2, "framework": 2, "pytest": 2, "discov": 2, "procedur": 2, "prefix": 2, "test_": 2, "ha": 2, "featur": 2, "assert": 2, "fixtur": 2, "along": 2, "numer": 2, "exampl": 2, "assist": 2, "start": 2, "independ": 2, "separ": 2, "command": [2, 3], "line": [2, 3], "In": 2, "root": 2, "work": 2, "ini": 2, "print": 2, "messag": 2, "dure": 2, "log_cli": 2, "log_cli_level": 2, "branchi": 2, "workflow": 2, "where": 2, "pr": 2, "made": 2, "merg": 2, "master": 2, "action": [2, 3], "suit": 2, "pass": 2, "process": [2, 3], "pre": 2, "commit": 2, "singl": 2, "config": 2, "yaml": 2, "both": 2, "ci": 2, "local": 2, "hook": 2, "doe": [2, 3], "manag": 2, "quick": 2, "guid": 2, "black": 2, "flake8": 2, "ensur": 2, "uncompromis": 2, "identifi": 2, "programmat": 2, "problem": 2, "auto": 2, "new": 2, "As": 2, "part": [2, 3], "secret": 2, "scanner": 2, "tufflehog3": 2, "also": [2, 3], "push": 2, "gh": 2, "page": 2, "api": [2, 3], "docstr": 2, "public": 2, "privat": 2, "trigger": 2, "tag": 2, "v": 2, "v0": 2, "v1": [2, 3], "0a1": 2, "0rc2": 2, "origin": 2, "semant": 2, "practic": 2, "guidelin": 2, "major": 2, "minor": 2, "patch": 2, "number": 2, "pep": 2, "440": 2, "identif": 2, "depend": 2, "specif": [2, 3], "cheat": 2, "without": 2, "post": 2, "suffix": 2, "setuptools_scm": 2, "introspect": 2, "hard": 2, "anywher": 2, "sphinx": 3, "found": 3, "http": 3, "github": 3, "tomoj": 3, "proper": 3, "publish": 3, "wheel": 3, "tarbal": 3, "git": 3, "manual": 3, "download": 3, "interfac": 3, "bcbb": 3, "pypi": 3, "host": 3, "actifactori": 3, "extra": 3, "index": 3, "howev": 3, "usernam": 3, "password": 3, "artifactori": 3, "tomojs_pytool": 3, "nih": 3, "gov": 3, "simpl": 3, "convention": 3, "setup": 3, "enforc": 3, "addition": 3, "script": 3, "altern": 3, "com": 3, "mac": 3, "m1": 3, "develop": 3, "imagecodec": 3, "osx": 3, "arm": 3, "binari": 3, "workaround": 3, "x86_64": 3, "zarr_rechunk": 3, "zarr_info": 3, "prerequisit": 3, "test": 3, "contribut": 3, "releas": 3}, "objects": {"": [[0, 0, 0, "-", "pytools"]], "pytools": [[0, 1, 1, "", "HedwigZarrImage"], [0, 1, 1, "", "HedwigZarrImages"], [0, 0, 0, "-", "convert"], [0, 0, 0, "-", "meta"], [0, 4, 1, "", "visual_min_max"], [0, 0, 0, "-", "zarr_build_multiscales"], [0, 4, 1, "", "zarr_extract_2d"], [0, 0, 0, "-", "zarr_rechunk"]], "pytools.HedwigZarrImage": [[0, 2, 1, "", "dims"], [0, 3, 1, "", "extract_2d"], [0, 3, 1, "", "neuroglancer_shader_parameters"], [0, 3, 1, "", "ome_roi_model"], [0, 2, 1, "", "path"], [0, 3, 1, "", "rechunk"], [0, 2, 1, "", "shader_type"], [0, 2, 1, "", "shape"], [0, 2, 1, "", "spacing"], [0, 2, 1, "", "units"]], "pytools.HedwigZarrImages": [[0, 3, 1, "", "get_series_keys"], [0, 3, 1, "", "group"], [0, 2, 1, "", "ome_info"], [0, 2, 1, "", "ome_xml_path"], [0, 3, 1, "", "series"]], "pytools.convert": [[0, 4, 1, "", "file_to_uint8"]], "pytools.meta": [[0, 4, 1, "", "is_int16"]], "pytools.utils": [[0, 0, 0, "-", "histogram"], [0, 0, 0, "-", "zarr"]], "pytools.utils.histogram": [[0, 1, 1, "", "DaskHistogramHelper"], [0, 1, 1, "", "HistogramBase"], [0, 1, 1, "", "ZARRHistogramHelper"], [0, 4, 1, "", "histogram_robust_stats"], [0, 4, 1, "", "histogram_stats"], [0, 4, 1, "", "weighted_quantile"]], "pytools.utils.zarr": [[0, 4, 1, "", "bin_shrink"], [0, 4, 1, "", "build_pyramid"]], "zarr_info": [[1, 5, 1, "cmdoption-zarr_info-log-level", "--log-level"], [1, 5, 1, "cmdoption-zarr_info-show", "--show"], [1, 5, 1, "cmdoption-zarr_info-version", "--version"], [1, 5, 1, "cmdoption-zarr_info-arg-INPUT_ZARR", "INPUT_ZARR"]], "zarr_rechunk": [[1, 5, 1, "cmdoption-zarr_rechunk-chunk-size", "--chunk-size"], [1, 5, 1, "cmdoption-zarr_rechunk-in-memory", "--in-memory"], [1, 5, 1, "cmdoption-zarr_rechunk-log-level", "--log-level"], [1, 5, 1, "cmdoption-zarr_rechunk-recompress", "--recompress"], [1, 5, 1, "cmdoption-zarr_rechunk-version", "--version"], [1, 5, 1, "cmdoption-zarr_rechunk-arg-INPUT_ZARR", "INPUT_ZARR"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:property", "3": "py:method", "4": "py:function", "5": "std:cmdoption"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "property", "Python property"], "3": ["py", "method", "Python method"], "4": ["py", "function", "Python function"], "5": ["std", "cmdoption", "program option"]}, "titleterms": {"api": 0, "command": 1, "line": 1, "interfac": 1, "zarr_rechunk": 1, "zarr_info": 1, "develop": 2, "prerequisit": 2, "github": 2, "com": 2, "git": 2, "lf": 2, "setup": 2, "test": 2, "run": 2, "unit": 2, "configur": 2, "contribut": 2, "lint": 2, "sphinx": 2, "document": [2, 3], "releas": 2, "version": 2, "welcom": 3, "pytool": 3, "": 3, "instal": 3, "content": 3}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 60}, "alltitles": {"API": [[0, "module-pytools"]], "Command Line Interface": [[1, "command-line-interface"]], "zarr_rechunk": [[1, "zarr-rechunk"]], "zarr_info": [[1, "zarr-info"]], "Development": [[2, "development"]], "Prerequisites": [[2, "prerequisites"]], "Github.com": [[2, "github.com"]], "Git LFS": [[2, "git-lfs"]], "Development Setup": [[2, "development-setup"]], "Testing": [[2, "testing"]], "Running Unit Tests": [[2, "running-unit-tests"]], "Test Configuration": [[2, "test-configuration"]], "Contributing": [[2, "contributing"]], "Linting": [[2, "linting"]], "Sphinx Documentation": [[2, "sphinx-documentation"]], "Releases": [[2, "releases"]], "Versioning": [[2, "versioning"]], "Welcome to pytools\u2019s documentation!": [[3, "welcome-to-pytools-s-documentation"]], "Installation": [[3, "installation"]], "Contents:": [[3, null]]}, "indexentries": {"daskhistogramhelper (class in pytools.utils.histogram)": [[0, "pytools.utils.histogram.DaskHistogramHelper"]], "hedwigzarrimage (class in pytools)": [[0, "pytools.HedwigZarrImage"]], "hedwigzarrimages (class in pytools)": [[0, "pytools.HedwigZarrImages"]], "histogrambase (class in pytools.utils.histogram)": [[0, "pytools.utils.histogram.HistogramBase"]], "zarrhistogramhelper (class in pytools.utils.histogram)": [[0, "pytools.utils.histogram.ZARRHistogramHelper"]], "bin_shrink() (in module pytools.utils.zarr)": [[0, "pytools.utils.zarr.bin_shrink"]], "build_pyramid() (in module pytools.utils.zarr)": [[0, "pytools.utils.zarr.build_pyramid"]], "dims (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.dims"]], "extract_2d() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.extract_2d"]], "file_to_uint8() (in module pytools.convert)": [[0, "pytools.convert.file_to_uint8"]], "get_series_keys() (pytools.hedwigzarrimages method)": [[0, "pytools.HedwigZarrImages.get_series_keys"]], "group() (pytools.hedwigzarrimages method)": [[0, "pytools.HedwigZarrImages.group"]], "histogram_robust_stats() (in module pytools.utils.histogram)": [[0, "pytools.utils.histogram.histogram_robust_stats"]], "histogram_stats() (in module pytools.utils.histogram)": [[0, "pytools.utils.histogram.histogram_stats"]], "is_int16() (in module pytools.meta)": [[0, "pytools.meta.is_int16"]], "module": [[0, "module-pytools"], [0, "module-pytools.convert"], [0, "module-pytools.meta"], [0, "module-pytools.utils.histogram"], [0, "module-pytools.utils.zarr"], [0, "module-pytools.zarr_build_multiscales"], [0, "module-pytools.zarr_rechunk"]], "neuroglancer_shader_parameters() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.neuroglancer_shader_parameters"]], "ome_info (pytools.hedwigzarrimages property)": [[0, "pytools.HedwigZarrImages.ome_info"]], "ome_roi_model() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.ome_roi_model"]], "ome_xml_path (pytools.hedwigzarrimages property)": [[0, "pytools.HedwigZarrImages.ome_xml_path"]], "path (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.path"]], "pytools": [[0, "module-pytools"]], "pytools.convert": [[0, "module-pytools.convert"]], "pytools.meta": [[0, "module-pytools.meta"]], "pytools.utils.histogram": [[0, "module-pytools.utils.histogram"]], "pytools.utils.zarr": [[0, "module-pytools.utils.zarr"]], "pytools.zarr_build_multiscales": [[0, "module-pytools.zarr_build_multiscales"]], "pytools.zarr_rechunk": [[0, "module-pytools.zarr_rechunk"]], "rechunk() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.rechunk"]], "series() (pytools.hedwigzarrimages method)": [[0, "pytools.HedwigZarrImages.series"]], "shader_type (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.shader_type"]], "shape (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.shape"]], "spacing (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.spacing"]], "units (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.units"]], "visual_min_max() (in module pytools)": [[0, "pytools.visual_min_max"]], "weighted_quantile() (in module pytools.utils.histogram)": [[0, "pytools.utils.histogram.weighted_quantile"]], "zarr_extract_2d() (in module pytools)": [[0, "pytools.zarr_extract_2d"]], "--chunk-size": [[1, "cmdoption-zarr_rechunk-chunk-size"]], "--in-memory": [[1, "cmdoption-zarr_rechunk-in-memory"]], "--log-level": [[1, "cmdoption-zarr_info-log-level"], [1, "cmdoption-zarr_rechunk-log-level"]], "--recompress": [[1, "cmdoption-zarr_rechunk-recompress"]], "--show": [[1, "cmdoption-zarr_info-show"]], "--version": [[1, "cmdoption-zarr_info-version"], [1, "cmdoption-zarr_rechunk-version"]], "input_zarr": [[1, "cmdoption-zarr_info-arg-INPUT_ZARR"], [1, "cmdoption-zarr_rechunk-arg-INPUT_ZARR"]], "zarr_info command line option": [[1, "cmdoption-zarr_info-arg-INPUT_ZARR"], [1, "cmdoption-zarr_info-log-level"], [1, "cmdoption-zarr_info-show"], [1, "cmdoption-zarr_info-version"]], "zarr_rechunk command line option": [[1, "cmdoption-zarr_rechunk-arg-INPUT_ZARR"], [1, "cmdoption-zarr_rechunk-chunk-size"], [1, "cmdoption-zarr_rechunk-in-memory"], [1, "cmdoption-zarr_rechunk-log-level"], [1, "cmdoption-zarr_rechunk-recompress"], [1, "cmdoption-zarr_rechunk-version"]]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API": [[0, "module-pytools"]], "Command Line Interface": [[1, "command-line-interface"]], "Contents:": [[3, null]], "Contributing": [[2, "contributing"]], "Development": [[2, "development"]], "Development Setup": [[2, "development-setup"]], "Git LFS": [[2, "git-lfs"]], "Github.com": [[2, "github.com"]], "Installation": [[3, "installation"]], "Linting": [[2, "linting"]], "Prerequisites": [[2, "prerequisites"]], "Releases": [[2, "releases"]], "Running Unit Tests": [[2, "running-unit-tests"]], "Sphinx Documentation": [[2, "sphinx-documentation"]], "Test Configuration": [[2, "test-configuration"]], "Testing": [[2, "testing"]], "Versioning": [[2, "versioning"]], "Welcome to pytools\u2019s documentation!": [[3, "welcome-to-pytools-s-documentation"]], "zarr_info": [[1, "zarr-info"]], "zarr_rechunk": [[1, "zarr-rechunk"]]}, "docnames": ["api", "commandline", "development", "index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["api.rst", "commandline.rst", "development.rst", "index.rst"], "indexentries": {"--chunk-size": [[1, "cmdoption-zarr_rechunk-chunk-size", false]], "--in-memory": [[1, "cmdoption-zarr_rechunk-in-memory", false]], "--log-level": [[1, "cmdoption-zarr_info-log-level", false], [1, "cmdoption-zarr_rechunk-log-level", false]], "--recompress": [[1, "cmdoption-zarr_rechunk-recompress", false]], "--show": [[1, "cmdoption-zarr_info-show", false]], "--version": [[1, "cmdoption-zarr_info-version", false], [1, "cmdoption-zarr_rechunk-version", false]], "bin_shrink() (in module pytools.utils.zarr)": [[0, "pytools.utils.zarr.bin_shrink", false]], "build_pyramid() (in module pytools.utils.zarr)": [[0, "pytools.utils.zarr.build_pyramid", false]], "daskhistogramhelper (class in pytools.utils.histogram)": [[0, "pytools.utils.histogram.DaskHistogramHelper", false]], "dims (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.dims", false]], "extract_2d() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.extract_2d", false]], "file_to_uint8() (in module pytools.convert)": [[0, "pytools.convert.file_to_uint8", false]], "get_series_keys() (pytools.hedwigzarrimages method)": [[0, "pytools.HedwigZarrImages.get_series_keys", false]], "group() (pytools.hedwigzarrimages method)": [[0, "pytools.HedwigZarrImages.group", false]], "hedwigzarrimage (class in pytools)": [[0, "pytools.HedwigZarrImage", false]], "hedwigzarrimages (class in pytools)": [[0, "pytools.HedwigZarrImages", false]], "histogram_robust_stats() (in module pytools.utils.histogram)": [[0, "pytools.utils.histogram.histogram_robust_stats", false]], "histogram_stats() (in module pytools.utils.histogram)": [[0, "pytools.utils.histogram.histogram_stats", false]], "histogrambase (class in pytools.utils.histogram)": [[0, "pytools.utils.histogram.HistogramBase", false]], "input_zarr": [[1, "cmdoption-zarr_info-arg-INPUT_ZARR", false], [1, "cmdoption-zarr_rechunk-arg-INPUT_ZARR", false]], "is_16bit() (in module pytools.meta)": [[0, "pytools.meta.is_16bit", false]], "is_int16() (in module pytools.meta)": [[0, "pytools.meta.is_int16", false]], "module": [[0, "module-pytools", false], [0, "module-pytools.convert", false], [0, "module-pytools.meta", false], [0, "module-pytools.utils.histogram", false], [0, "module-pytools.utils.zarr", false], [0, "module-pytools.zarr_build_multiscales", false], [0, "module-pytools.zarr_rechunk", false]], "neuroglancer_shader_parameters() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.neuroglancer_shader_parameters", false]], "ome_info (pytools.hedwigzarrimages property)": [[0, "pytools.HedwigZarrImages.ome_info", false]], "ome_roi_model() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.ome_roi_model", false]], "ome_xml_path (pytools.hedwigzarrimages property)": [[0, "pytools.HedwigZarrImages.ome_xml_path", false]], "path (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.path", false]], "pytools": [[0, "module-pytools", false]], "pytools.convert": [[0, "module-pytools.convert", false]], "pytools.meta": [[0, "module-pytools.meta", false]], "pytools.utils.histogram": [[0, "module-pytools.utils.histogram", false]], "pytools.utils.zarr": [[0, "module-pytools.utils.zarr", false]], "pytools.zarr_build_multiscales": [[0, "module-pytools.zarr_build_multiscales", false]], "pytools.zarr_rechunk": [[0, "module-pytools.zarr_rechunk", false]], "rechunk() (pytools.hedwigzarrimage method)": [[0, "pytools.HedwigZarrImage.rechunk", false]], "series() (pytools.hedwigzarrimages method)": [[0, "pytools.HedwigZarrImages.series", false]], "shader_type (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.shader_type", false]], "shape (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.shape", false]], "spacing (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.spacing", false]], "units (pytools.hedwigzarrimage property)": [[0, "pytools.HedwigZarrImage.units", false]], "visual_min_max() (in module pytools)": [[0, "pytools.visual_min_max", false]], "weighted_quantile() (in module pytools.utils.histogram)": [[0, "pytools.utils.histogram.weighted_quantile", false]], "zarr_extract_2d() (in module pytools)": [[0, "pytools.zarr_extract_2d", false]], "zarr_info command line option": [[1, "cmdoption-zarr_info-arg-INPUT_ZARR", false], [1, "cmdoption-zarr_info-log-level", false], [1, "cmdoption-zarr_info-show", false], [1, "cmdoption-zarr_info-version", false]], "zarr_rechunk command line option": [[1, "cmdoption-zarr_rechunk-arg-INPUT_ZARR", false], [1, "cmdoption-zarr_rechunk-chunk-size", false], [1, "cmdoption-zarr_rechunk-in-memory", false], [1, "cmdoption-zarr_rechunk-log-level", false], [1, "cmdoption-zarr_rechunk-recompress", false], [1, "cmdoption-zarr_rechunk-version", false]], "zarrhistogramhelper (class in pytools.utils.histogram)": [[0, "pytools.utils.histogram.ZARRHistogramHelper", false]]}, "objects": {"": [[0, 0, 0, "-", "pytools"]], "pytools": [[0, 1, 1, "", "HedwigZarrImage"], [0, 1, 1, "", "HedwigZarrImages"], [0, 0, 0, "-", "convert"], [0, 0, 0, "-", "meta"], [0, 4, 1, "", "visual_min_max"], [0, 0, 0, "-", "zarr_build_multiscales"], [0, 4, 1, "", "zarr_extract_2d"], [0, 0, 0, "-", "zarr_rechunk"]], "pytools.HedwigZarrImage": [[0, 2, 1, "", "dims"], [0, 3, 1, "", "extract_2d"], [0, 3, 1, "", "neuroglancer_shader_parameters"], [0, 3, 1, "", "ome_roi_model"], [0, 2, 1, "", "path"], [0, 3, 1, "", "rechunk"], [0, 2, 1, "", "shader_type"], [0, 2, 1, "", "shape"], [0, 2, 1, "", "spacing"], [0, 2, 1, "", "units"]], "pytools.HedwigZarrImages": [[0, 3, 1, "", "get_series_keys"], [0, 3, 1, "", "group"], [0, 2, 1, "", "ome_info"], [0, 2, 1, "", "ome_xml_path"], [0, 3, 1, "", "series"]], "pytools.convert": [[0, 4, 1, "", "file_to_uint8"]], "pytools.meta": [[0, 4, 1, "", "is_16bit"], [0, 4, 1, "", "is_int16"]], "pytools.utils": [[0, 0, 0, "-", "histogram"], [0, 0, 0, "-", "zarr"]], "pytools.utils.histogram": [[0, 1, 1, "", "DaskHistogramHelper"], [0, 1, 1, "", "HistogramBase"], [0, 1, 1, "", "ZARRHistogramHelper"], [0, 4, 1, "", "histogram_robust_stats"], [0, 4, 1, "", "histogram_stats"], [0, 4, 1, "", "weighted_quantile"]], "pytools.utils.zarr": [[0, 4, 1, "", "bin_shrink"], [0, 4, 1, "", "build_pyramid"]], "zarr_info": [[1, 5, 1, "cmdoption-zarr_info-log-level", "--log-level"], [1, 5, 1, "cmdoption-zarr_info-show", "--show"], [1, 5, 1, "cmdoption-zarr_info-version", "--version"], [1, 5, 1, "cmdoption-zarr_info-arg-INPUT_ZARR", "INPUT_ZARR"]], "zarr_rechunk": [[1, 5, 1, "cmdoption-zarr_rechunk-chunk-size", "--chunk-size"], [1, 5, 1, "cmdoption-zarr_rechunk-in-memory", "--in-memory"], [1, 5, 1, "cmdoption-zarr_rechunk-log-level", "--log-level"], [1, 5, 1, "cmdoption-zarr_rechunk-recompress", "--recompress"], [1, 5, 1, "cmdoption-zarr_rechunk-version", "--version"], [1, 5, 1, "cmdoption-zarr_rechunk-arg-INPUT_ZARR", "INPUT_ZARR"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "property", "Python property"], "3": ["py", "method", "Python method"], "4": ["py", "function", "Python function"], "5": ["std", "cmdoption", "program option"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:property", "3": "py:method", "4": "py:function", "5": "std:cmdoption"}, "terms": {"": 2, "0": [0, 2], "0a1": 2, "0rc2": 2, "1": [0, 2], "1024x1024": 1, "16": 0, "19": 0, "2": [0, 3], "255": 0, "2d": 0, "3": [0, 3], "4": 0, "440": 2, "5": 0, "64": 1, "8": 0, "9": 0, "A": [0, 2], "As": 2, "For": [0, 2], "If": 0, "In": 2, "Or": 1, "Such": 0, "The": [0, 1, 2, 3], "Will": 0, "With": 1, "__init__": 0, "_ome_idx": 0, "_ome_info": 0, "about": [0, 2], "absolut": 0, "access": 0, "account": 2, "actifactori": 3, "action": [2, 3], "activ": 2, "ad": 2, "addit": 0, "addition": 3, "algorithm": 0, "all": [0, 2], "along": 2, "also": [2, 3], "altern": 3, "an": [0, 1, 3], "annot": 0, "antialias": 0, "anystr": 0, "anywher": 2, "api": [2, 3], "appli": 0, "ar": [0, 2, 3], "argument": [1, 3], "arm": 3, "arr": 0, "arrai": 0, "artifactori": 3, "aspect": 0, "assert": 2, "assist": 2, "assum": 0, "auto": 2, "auto_uint8": 0, "automat": [0, 2], "avail": [0, 1], "averag": 0, "avoid": 0, "ax": 0, "axi": 0, "base": [2, 3], "bcbb": 3, "befor": [0, 2], "between": 0, "bin": [0, 2], "bin_edg": 0, "bin_shrink": [0, 3], "binari": 3, "bit": 0, "black": 2, "bool": 0, "both": 2, "branch": 2, "branchi": 2, "build_pyramid": [0, 3], "can": [0, 1, 2, 3], "case": 0, "chang": [0, 2], "channel": 0, "cheat": 2, "chunk": [0, 1], "chunk_siz": [0, 1], "ci": 2, "clamp": 0, "class": 0, "clone": 2, "close": 0, "code": 2, "collaps": 0, "com": 3, "command": [2, 3], "commit": 2, "commonli": 0, "compon": [0, 2], "compressor": [0, 1], "comput": 0, "config": 2, "configur": [0, 3], "consid": 0, "consist": 0, "contain": [0, 1, 2, 3], "contribut": 3, "convention": 3, "convers": 0, "convert": 0, "correct": 0, "count": 0, "creat": 2, "ct": 0, "current": [0, 2, 3], "dask": 0, "daskhistogramhelp": [0, 3], "data": [0, 2], "debug": [1, 2], "default": [0, 1, 2], "densiti": 0, "depend": 2, "describ": 1, "detail": [0, 2], "detect": 0, "determin": [0, 2], "dev": 2, "develop": 3, "deviat": 0, "dict": 0, "dictionari": 0, "differ": 0, "dim": 0, "dimens": [0, 1], "directli": [0, 1], "directori": [0, 2], "dirnam": 0, "discov": 2, "displai": 1, "doc": 2, "docstr": 2, "doe": [2, 3], "done": 0, "download": 3, "driver": 2, "duplic": 2, "dure": 2, "e": [0, 2], "each": 0, "edg": 0, "edit": 2, "either": 1, "element": 0, "empti": 0, "enforc": 3, "enough": 0, "ensur": 2, "enterpris": 2, "entir": 0, "entri": 1, "environ": 2, "error": 1, "estim": 0, "etc": 0, "exampl": 2, "execut": [1, 2, 3], "exist": 0, "exit": [1, 3], "extens": 0, "extra": 3, "extract": 0, "extract_2d": 0, "factor": 0, "fals": [0, 1], "faster": 0, "fastest": 0, "featur": 2, "file": [0, 2], "file_path": 0, "file_to_uint8": [0, 3], "filenam": 0, "first": 0, "fit": 0, "fixtur": 2, "flake8": 2, "float": 0, "floor": 0, "follow": [0, 1, 2], "format": [0, 2], "former": 0, "found": 3, "framework": 2, "from": [0, 2, 3], "full": 0, "function": 1, "g": 0, "gener": 0, "get": [0, 2], "get_series_kei": 0, "gh": 2, "git": 3, "gitattribut": 2, "github": 3, "given": 0, "global": 0, "gov": 3, "grayscal": 0, "greater": 0, "group": 0, "guid": 2, "guidelin": 2, "ha": 2, "hard": 2, "have": [0, 2], "header": 0, "hedwig": [0, 3], "hedwigzarrimag": [0, 3], "help": 1, "here": [2, 3], "hist": 0, "histogram": 0, "histogram_robust_stat": [0, 3], "histogram_stat": [0, 3], "histogrambas": [0, 3], "hold": 0, "hook": 2, "host": 3, "hostedtoolcach": 0, "howev": 3, "http": 3, "i": [0, 2, 3], "identif": 2, "identifi": 2, "imag": [0, 1, 2, 3], "imagecodec": 3, "imageio": 0, "imagezarrimag": 0, "img": 0, "implement": 0, "in_file_path": 0, "in_memori": 0, "includ": [0, 2, 3], "increas": 0, "independ": 2, "index": 3, "info": 1, "inform": 0, "ini": 2, "initi": [0, 2], "inplac": 0, "input": 0, "input_file_path": 0, "input_imag": 0, "input_zarr": [0, 1], "insight": 0, "inspect": 0, "instal": 2, "int": 0, "integ": 0, "integr": 2, "intens": 0, "interfac": 3, "introspect": 2, "invok": 1, "io": [0, 3], "is_16bit": [0, 3], "is_int16": [0, 3], "item": 0, "iter": 0, "itk": 0, "jpeg": 0, "json": 0, "kei": 0, "label": 0, "label_imag": 0, "larg": 2, "larger": 2, "length": 0, "level": 1, "lib": 0, "like": 0, "limit": 0, "line": [2, 3], "linearli": 0, "list": 0, "load": 0, "local": 2, "locat": 2, "log": [1, 2], "log_cli": 2, "log_cli_level": 2, "log_level": 1, "lower": 0, "m": [1, 2, 3], "m1": 3, "mac": 3, "mad": 0, "mad_scal": 0, "made": 2, "mai": 0, "maintain": 0, "major": 2, "manag": 2, "mani": [0, 2], "manual": 3, "master": 2, "maximum": 0, "mean": 0, "median": 0, "member": [0, 2], "memori": [0, 1], "merg": 2, "messag": 2, "meta": 0, "metadata": 0, "method": [1, 2], "middle_quantil": 0, "mii": 0, "minimum": 0, "minor": 2, "mode": 2, "model": [0, 2], "modul": [0, 1, 2], "mrc": 0, "multichannel": 0, "multipl": 0, "must": [0, 2], "name": 0, "need": [0, 2, 3], "neuroglanc": 0, "neuroglancer_shader_paramet": 0, "neuroglancerprecomputedfloor": 0, "neuroglancerprecomputedlimit": 0, "neuroglancerprecomputedmax": 0, "neuroglancerprecomputedmin": 0, "new": 2, "ngff": 0, "niaid": [2, 3], "nih": 3, "none": 0, "note": [0, 3], "number": 2, "numer": 2, "numpi": 0, "object": 0, "old_styl": 0, "om": 0, "ome_info": 0, "ome_roi_model": 0, "ome_xml_path": 0, "omeinfo": 0, "omeroimodel": 0, "onc": 2, "one": 0, "onli": [0, 2], "oper": [0, 2], "opt": 0, "option": [0, 1, 2, 3], "order": [0, 3], "organ": 2, "origin": 2, "osx": 3, "other": [0, 2], "otherwis": 0, "out_file_path": 0, "output": 0, "output_filenam": 0, "overwrit": 0, "packag": [0, 1, 2, 3], "page": 2, "parallel": 0, "paramet": 0, "pars": 0, "part": [2, 3], "pass": 2, "password": 3, "patch": 2, "path": 0, "pep": 2, "percentil": 0, "perform": 0, "pip": [2, 3], "pipelin": 0, "pixel": 0, "pkg": 2, "place": [0, 2], "pleas": 2, "png": 0, "point": [0, 1], "portion": 0, "post": 2, "pr": 2, "practic": 2, "pre": 2, "prefer": 1, "prefix": 2, "prerequisit": 3, "print": 2, "privat": 2, "problem": 2, "procedur": 2, "process": [2, 3], "produc": 0, "programmat": 2, "project": [2, 3], "proper": 3, "properti": 0, "provid": [0, 2, 3], "public": 2, "publish": 3, "push": 2, "py": [0, 3], "pypi": 3, "pyramid": 0, "pytest": 2, "python": [0, 1, 2, 3], "python3": [0, 3], "pytool": [0, 1, 2], "quantil": 0, "quick": 2, "r": 2, "rang": 0, "ratio": 0, "read": [0, 2], "read_onli": 0, "rechunk": 0, "recommend": [0, 2], "recompress": 1, "rectangl": 0, "reduc": 0, "relat": 2, "releas": 3, "remain": 0, "render": [0, 2], "repositori": [2, 3], "repres": 0, "requir": [0, 1, 2, 3], "resiz": 0, "resolut": [0, 1], "result": 0, "return": 0, "revers": 0, "rgb": 0, "robust": 0, "roi": 0, "root": 2, "round": 0, "same": 0, "sampl": 0, "sample_weight": 0, "scale": 0, "scanner": 2, "schedul": 0, "script": 3, "second": 0, "secret": 2, "section": [1, 2], "select": [0, 2], "semant": 2, "separ": 2, "seri": 0, "serial": 0, "set": [0, 2], "setup": 3, "setuptools_scm": 2, "shader": 0, "shader_typ": 0, "shaderparamet": 0, "shape": 0, "shift": 0, "should": [0, 2], "show": 1, "shrink": 0, "shrink_dim": 0, "sigma": 0, "sign": 0, "simpl": 3, "simpleitk": [0, 1], "singl": 2, "site": 0, "size": [0, 1], "size_factor": 0, "slowest": 0, "so": [0, 3], "sort": 0, "sourc": [0, 2], "space": 0, "spacial": 0, "spatial": 1, "specif": [2, 3], "specifi": [0, 3], "sphinx": 3, "standard": 0, "start": 2, "statist": 0, "storag": 2, "store": [0, 1, 2], "str": 0, "string": 0, "structur": 0, "sub": 1, "subdirectori": 0, "subvolum": 0, "suffix": 2, "suit": 2, "suitabl": 0, "support": 0, "system": 2, "tag": 2, "tarbal": 3, "target": 0, "target_size_i": 0, "target_size_x": 0, "task": 1, "test": 3, "test_": 2, "text": 2, "than": 0, "thei": [0, 1, 2, 3], "them": 2, "thi": [0, 2, 3], "tiff": 0, "time": [0, 3], "tomoj": 3, "tomojs_pytool": 3, "tool": 2, "toolkit": 0, "train": 2, "transpar": 2, "trigger": 2, "true": 0, "truncat": 0, "tufflehog3": 2, "tupl": 0, "two": 0, "txt": [2, 3], "type": 0, "uint16": 0, "uint8": 0, "uncompress": 0, "uncompromis": 2, "union": 0, "unit": 0, "unsign": 0, "up": 2, "upper": 0, "us": [0, 1, 2, 3], "usag": 2, "user": 2, "usernam": 3, "usual": 2, "util": [0, 3], "v": 2, "v0": 2, "v1": [2, 3], "valu": 0, "values_sort": 0, "var": 0, "varianc": 0, "variou": 1, "venv": 2, "veri": 0, "version": [1, 3], "virtual": 2, "visibl": 0, "visual": 0, "visual_min_max": [0, 3], "wai": 1, "warn": 1, "weight": 0, "weighted_quantil": [0, 3], "wheel": 3, "when": [1, 2], "where": 2, "which": [0, 2], "while": 0, "without": 2, "work": 2, "workaround": 3, "workflow": 2, "would": 0, "write": [0, 2], "written": 0, "x": 0, "x64": 0, "x86_64": 3, "xml": 0, "xy": 0, "xyc": 0, "xyz": 0, "xyzct": 0, "y": 0, "yaml": 2, "z": 0, "zarr": [0, 1], "zarr_extract_2d": [0, 3], "zarr_grp": 0, "zarr_info": 3, "zarr_path": 0, "zarr_rechunk": 3, "zarrai": 0, "zarrhistogramhelp": [0, 3], "zct": 0}, "titles": ["API", "Command Line Interface", "Development", "Welcome to pytools\u2019s documentation!"], "titleterms": {"": 3, "api": 0, "com": 2, "command": 1, "configur": 2, "content": 3, "contribut": 2, "develop": 2, "document": [2, 3], "git": 2, "github": 2, "instal": 3, "interfac": 1, "lf": 2, "line": 1, "lint": 2, "prerequisit": 2, "pytool": 3, "releas": 2, "run": 2, "setup": 2, "sphinx": 2, "test": 2, "unit": 2, "version": 2, "welcom": 3, "zarr_info": 1, "zarr_rechunk": 1}}) \ No newline at end of file