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diff --git a/_modules/gridData/core.html b/_modules/gridData/core.html
index 048b805..b79070f 100644
--- a/_modules/gridData/core.html
+++ b/_modules/gridData/core.html
@@ -14,29 +14,27 @@
+
+
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+ gridData.core — GridDataFormats 1.0.2+8.g86a4109 documentation
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@@ -1097,7 +1095,7 @@ Source code for gridData.core
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diff --git a/_modules/gridData/gOpenMol.html b/_modules/gridData/gOpenMol.html
index 47d6b72..baca24c 100644
--- a/_modules/gridData/gOpenMol.html
+++ b/_modules/gridData/gOpenMol.html
@@ -14,29 +14,27 @@
+
+
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+ gridData.gOpenMol — GridDataFormats 1.0.2+8.g86a4109 documentation
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diff --git a/_modules/gridData/mrc.html b/_modules/gridData/mrc.html
index 68fd6aa..7429e96 100644
--- a/_modules/gridData/mrc.html
+++ b/_modules/gridData/mrc.html
@@ -14,29 +14,27 @@
+
+
- gridData.mrc — GridDataFormats 1.0.2+7.g020b199 documentation
+ gridData.mrc — GridDataFormats 1.0.2+8.g86a4109 documentation
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@@ -316,7 +314,7 @@ Source code for gridData.mrc
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diff --git a/_modules/index.html b/_modules/index.html
index 85d0056..fe21c47 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -14,29 +14,27 @@
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- Overview: module code — GridDataFormats 1.0.2+7.g020b199 documentation
+ Overview: module code — GridDataFormats 1.0.2+8.g86a4109 documentation
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@@ -158,7 +156,7 @@ All modules for which code is available
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diff --git a/_static/basic.css b/_static/basic.css
index 30fee9d..7ebbd6d 100644
--- a/_static/basic.css
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/*
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/* -- search page ----------------------------------------------------------- */
ul.search {
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ul.search li {
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diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css
index c718cee..88ba55b 100644
--- a/_static/css/badge_only.css
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diff --git a/_static/doctools.js b/_static/doctools.js
index d06a71d..0398ebb 100644
--- a/_static/doctools.js
+++ b/_static/doctools.js
@@ -1,12 +1,5 @@
/*
- * doctools.js
- * ~~~~~~~~~~~
- *
* Base JavaScript utilities for all Sphinx HTML documentation.
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- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
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"use strict";
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index 0c34624..5846319 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
- VERSION: '1.0.2+7.g020b199',
+ VERSION: '1.0.2+8.g86a4109',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
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index 2b43bd0..0000000
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+++ /dev/null
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-* @preserve HTML5 Shiv 3.7.3-pre | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
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GridDataFormats
- Search GridDataFormats 1.0.2+7.g020b199 documentation
+ Search GridDataFormats 1.0.2+8.g86a4109 documentation
utf-8
GridDataFormats 1.0.2+7.g020b199 documentation
+ GridDataFormats 1.0.2+8.g86a4109 documentation
\ No newline at end of file
diff --git a/_static/searchtools.js b/_static/searchtools.js
index 7918c3f..2c774d1 100644
--- a/_static/searchtools.js
+++ b/_static/searchtools.js
@@ -1,12 +1,5 @@
/*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
* Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
"use strict";
@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") {
// and returns the new score.
/*
score: result => {
- const [docname, title, anchor, descr, score, filename] = result
+ const [docname, title, anchor, descr, score, filename, kind] = result
return score
},
*/
@@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") {
};
}
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+ static get index() { return "index"; }
+ static get object() { return "object"; }
+ static get text() { return "text"; }
+ static get title() { return "title"; }
+}
+
const _removeChildren = (element) => {
while (element && element.lastChild) element.removeChild(element.lastChild);
};
@@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;
- const [docName, title, anchor, descr, score, _filename] = item;
+ const [docName, title, anchor, descr, score, _filename, kind] = item;
let listItem = document.createElement("li");
+ // Add a class representing the item's type:
+ // can be used by a theme's CSS selector for styling
+ // See SearchResultKind for the class names.
+ listItem.classList.add(`kind-${kind}`);
let requestUrl;
let linkUrl;
if (docBuilder === "dirhtml") {
@@ -99,7 +104,7 @@ 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
@@ -115,9 +120,11 @@ const _finishSearch = (resultCount) => {
"Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
);
else
- Search.status.innerText = _(
- `Search finished, found ${resultCount} page(s) matching the search query.`
- );
+ Search.status.innerText = Documentation.ngettext(
+ "Search finished, found one page matching the search query.",
+ "Search finished, found ${resultCount} pages matching the search query.",
+ resultCount,
+ ).replace('${resultCount}', resultCount);
};
const _displayNextItem = (
results,
@@ -137,6 +144,22 @@ 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, kind].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+ const leftScore = a[4];
+ const rightScore = b[4];
+ if (leftScore === rightScore) {
+ // same score: sort alphabetically
+ const leftTitle = a[1].toLowerCase();
+ const rightTitle = b[1].toLowerCase();
+ if (leftTitle === rightTitle) return 0;
+ return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+ }
+ return leftScore > rightScore ? 1 : -1;
+};
/**
* Default splitQuery function. Can be overridden in ``sphinx.search`` with a
@@ -160,13 +183,26 @@ 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 [".headerlink", "script", "style"]) {
+ htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+ }
+ if (anchor) {
+ const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+ if (anchorContent) return anchorContent.textContent;
+
+ console.warn(
+ `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+ );
+ }
+
+ // if anchor not specified or not found, fall back to main content
const docContent = htmlElement.querySelector('[role="main"]');
- if (docContent !== 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 "";
},
@@ -219,6 +255,7 @@ const Search = {
searchSummary.classList.add("search-summary");
searchSummary.innerText = "";
const searchList = document.createElement("ul");
+ searchList.setAttribute("role", "list");
searchList.classList.add("search");
const out = document.getElementById("search-results");
@@ -239,16 +276,7 @@ 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();
@@ -284,22 +312,40 @@ 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, kind].
+ 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([
+ const score = Math.round(Scorer.title * queryLower.length / title.length);
+ const boost = titles[file] === title ? 1 : 0; // add a boost for document titles
+ normalResults.push([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
null,
- score,
+ score + boost,
filenames[file],
+ SearchResultKind.title,
]);
}
}
@@ -308,46 +354,48 @@ 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],
- ]);
+ SearchResultKind.index,
+ ];
+ 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 +409,12 @@ 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
@@ -432,6 +485,7 @@ const Search = {
descr,
score,
filenames[match[0]],
+ SearchResultKind.object,
]);
};
Object.keys(objects).forEach((prefix) =>
@@ -466,14 +520,18 @@ 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 +554,8 @@ 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);
});
});
@@ -539,6 +596,7 @@ const Search = {
null,
score,
filenames[file],
+ SearchResultKind.text,
]);
}
return results;
@@ -549,8 +607,8 @@ 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/genindex.html b/genindex.html
index 758d587..b9d8546 100644
--- a/genindex.html
+++ b/genindex.html
@@ -14,29 +14,27 @@
+
+
- Index — GridDataFormats 1.0.2+7.g020b199 documentation
+ Index — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -484,7 +482,7 @@ W
aria-label="versions">
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/basic.html b/gridData/basic.html
index 9f00347..bd5132f 100644
--- a/gridData/basic.html
+++ b/gridData/basic.html
@@ -14,30 +14,28 @@
+
+
- Basic use — GridDataFormats 1.0.2+7.g020b199 documentation
+ Basic use — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -147,7 +145,7 @@ Loading datag = Grid("density.plt")
-From the output of numpy.histogramdd():
+From the output of numpy.histogramdd():
import numpy
r = numpy.random.randn(100,3)
H, edges = np.histogramdd(r, bins = (5, 8, 4))
@@ -264,7 +262,7 @@ Resampling
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/core.html b/gridData/core.html
index fd2204b..47cb56d 100644
--- a/gridData/core.html
+++ b/gridData/core.html
@@ -14,31 +14,29 @@
+
+
- Core functionality for storing n-D grids — gridData.core — GridDataFormats 1.0.2+7.g020b199 documentation
+ Core functionality for storing n-D grids — gridData.core — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
@@ -177,20 +175,20 @@ Classes and functions
Parameters:
-grid (numpy.ndarray or str (optional)) – Build the grid either from a histogram or density (a numpy nD
+
grid (numpy.ndarray or str (optional)) – Build the grid either from a histogram or density (a numpy nD
array) or read data from a filename.
edges (list (optional)) – List of arrays, the lower and upper bin edges along the axes
-(same as the output by numpy.histogramdd())
origin (numpy.ndarray (optional)) – Cartesian coordinates of the center of grid position at index
+
edges (list (optional)) – List of arrays, the lower and upper bin edges along the axes
+(same as the output by numpy.histogramdd())
origin (numpy.ndarray (optional)) – Cartesian coordinates of the center of grid position at index
[0, 0, ..., 0].
delta (numpy.ndarray (optional)) – Either n x n array containing the cell lengths in each dimension,
+
delta (numpy.ndarray (optional)) – Either n x n array containing the cell lengths in each dimension,
or n x 1 array for rectangular arrays.
metadata (dict (optional)) – A user defined dictionary of arbitrary key/value pairs
+
metadata (dict (optional)) – A user defined dictionary of arbitrary key/value pairs
associated with the density; the class does not touch
metadata but stores it with save()
interpolation_spline_order (int (optional)) – Order of interpolation function for resampling with
+
interpolation_spline_order (int (optional)) – Order of interpolation function for resampling with
resample(); cubic splines = 3 and the default is 3
file_format (str (optional)) – Name of the file format; only necessary when grid is a
+
file_format (str (optional)) – Name of the file format; only necessary when grid is a
filename (see load()) and autodetection of the file
format fails. The default is None and normally the file
format is guessed from the file extension.
Classes and functions
- Raises:
-TypeError – If the dimensions of the various input data do not agree with
+
TypeError – If the dimensions of the various input data do not agree with
each other.
ValueError – If some of the required data are not provided in the keyword
+
ValueError – If some of the required data are not provided in the keyword
arguments, e.g., if only the grid is supplied as an array but
not the edges or only grid and one of origin and delta.
NotImplementedError – If triclinic (non-orthorhombic) boxes are supplied in delta
+
NotImplementedError – If triclinic (non-orthorhombic) boxes are supplied in delta
.. Note:: delta can only be a 1D array of length grid.ndim
@@ -220,7 +218,7 @@ Classes and functions\(y\) component, and axis 2 to the \(z\) component.
- Type:
--
+
-
Classes and functionsGrid.grid.ndim.
- Type:
--
+
-
Classes and functionscenter of cell Grid.grid[0, 0, .., 0].
- Type:
--
+
-
@@ -263,7 +261,7 @@ Classes and functionsGrid.delta[i] for axis i.
@@ -276,7 +274,7 @@ Classes and functions
@@ -289,14 +287,14 @@ Classes and functionssave().
Example
Create a Grid object from data.
-From numpy.histogramdd():
+From numpy.histogramdd():
grid, edges = numpy.histogramdd(...)
g = Grid(grid, edges=edges)
@@ -351,11 +349,11 @@ Classes and functionsresample().
- Parameters:
-other (Grid or float or int) – Another object to be used for standard arithmetic
+
other (Grid or float or int) – Another object to be used for standard arithmetic
operations with this Grid
- Raises:
-TypeError – if not compatible
+TypeError – if not compatible
@@ -389,22 +387,22 @@ Classes and functions
Parameters:
-filename (str) – name of the output file
filename (str) – name of the output file
file_format ({'dx', 'pickle', None} (optional)) – output file format, the default is “dx”
type (str (optional)) –
for DX, set the output DX array type, e.g., “double” or “float”.
+
type (str (optional)) –
for DX, set the output DX array type, e.g., “double” or “float”.
By default (None), the DX type is determined from the numpy
dtype of the array of the grid (and this will typically result in
“double”).
-New in version 0.4.0.
+Added in version 0.4.0.
typequote (str (optional)) –
For DX, set the character used to quote the type string;
+
typequote (str (optional)) –
For DX, set the character used to quote the type string;
by default this is a double-quote character, ‘”’.
Custom parsers like the one from NAMD-GridForces (backend for MDFF)
expect no quotes, and typequote=’’ may be used to appease them.
-New in version 0.5.0.
+Added in version 0.5.0.
@@ -441,7 +439,7 @@ Classes and functions
-Internally, the function uses scipy.ndimage.map_coordinates()
+
Internally, the function uses scipy.ndimage.map_coordinates()
with mode="constant" whereby interpolated values outside
the interpolated grid are determined by filling all values beyond
the edge with the same constant value, defined by the
@@ -461,7 +459,7 @@
Classes and functionsOrder of the B-spline interpolation of the data.
3 = cubic; 4 & 5 are also supported
Only choose values that are acceptable to
-scipy.ndimage.spline_filter()!
+scipy.ndimage.spline_filter()!
See also
@@ -487,7 +485,7 @@ Classes and functionsbefore calling resample().
- Parameters:
-edges (tuple of arrays or Grid) – edges of the new grid or a Grid instance that
+
edges (tuple of arrays or Grid) – edges of the new grid or a Grid instance that
provides Grid.edges
- Returns:
@@ -518,7 +516,7 @@ Classes and functionsResample to a new regular grid.
- Parameters:
-factor (float) – The number of grid cells are scaled with factor in each
+
factor (float) – The number of grid cells are scaled with factor in each
dimension, i.e., factor * N_i cells along each
dimension i. Must be positive, and cannot result in fewer
than 2 cells along a dimension.
@@ -615,7 +613,7 @@ Classes and functions
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/formats.html b/gridData/formats.html
index ff5f8b8..fc246cc 100644
--- a/gridData/formats.html
+++ b/gridData/formats.html
@@ -14,30 +14,29 @@
+
+
- Formats — GridDataFormats 1.0.2+7.g020b199 documentation
+ Formats — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
@@ -258,7 +257,7 @@ Format-specific modules
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/formats/OpenDX.html b/gridData/formats/OpenDX.html
index 493df6a..7c08010 100644
--- a/gridData/formats/OpenDX.html
+++ b/gridData/formats/OpenDX.html
@@ -14,31 +14,29 @@
+
+
- OpenDX — routines to read and write simple OpenDX files — GridDataFormats 1.0.2+7.g020b199 documentation
+ OpenDX — routines to read and write simple OpenDX files — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
@@ -247,7 +245,7 @@ Known issues for writing OpenDX filestype="double".
-New in version 0.4.0.
+Added in version 0.4.0.
@@ -274,7 +272,7 @@ Building a dx object from a numpy array numpy.dtype
of the numpy.ndarray that is provided as
+numpy.dtype of the numpy.ndarray that is provided as
the grid (or with the type keyword argument to
gridData.OpenDX.array).
For example, to build a field:
@@ -300,11 +298,11 @@ Building a dx object from a dx filenumpy.ndarray in the dx.components[‘data’].array with the
-numpy.dtype determined by the DX type in the file.
+numpy.ndarray in the dx.components[‘data’].array with the
+numpy.dtype determined by the DX type in the file.
The dx field object has a method
histogramdd() that produces output identical to
-the numpy.histogramdd() function by taking the stored dimension
+the numpy.histogramdd() function by taking the stored dimension
and deltas into account. In this way, one can store nD histograms in a
portable and universal manner:
histogram, edges = dx.histogramdd()
@@ -445,28 +443,28 @@ Classes and functions
- Parameters:
-classid (int) –
array (array_like) –
type (str (optional)) –
Set the DX type in the output file and cast array to
+
classid (int)
array (array_like)
type (str (optional)) –
Set the DX type in the output file and cast array to
the closest numpy dtype. type must be one of the
allowed types in DX files as defined under Array
Objects. The default None tries to set the type
-from the numpy.dtype of array.
+from the numpy.dtype of array.
-New in version 0.4.0.
+Added in version 0.4.0.
- Raises:
-ValueError – if array is not provided; or if type is not of the correct
+
ValueError – if array is not provided; or if type is not of the correct
DX type
-
dx_types = {'byte': 'uint8', 'double': 'float64', 'float': 'float32', 'int': 'int32', 'short': 'int16', 'signed byte': 'int8', 'signed int': 'int32', 'signed short': 'int16', 'unsigned byte': 'uint8', 'unsigned int': 'uint32', 'unsigned short': 'uint16'}
-conversion from OpenDX type to closest numpy.dtype
+
conversion from OpenDX type to closest numpy.dtype
(round-tripping is not guaranteed to produce identical types); not all
types are supported (e.g., strings and conversion to int64 are missing)
@@ -474,7 +472,7 @@ Classes and functions
-
np_types = {'float16': 'float', 'float32': 'float', 'float64': 'double', 'int16': 'short', 'int32': 'int', 'int64': 'int', 'int8': 'signed byte', 'uint16': 'unsigned short', 'uint32': 'unsigned int', 'uint64': 'unsigned int', 'uint8': 'byte'}
-conversion from numpy.dtype.name to closest OpenDX array type
+
conversion from numpy.dtype.name to closest OpenDX array type
(round-tripping is not guaranteed to produce identical types); not all
types are supported (e.g., strings are missing)
Classes and functionsWrite the class array section.
- Parameters:
-stream (stream) –
+stream (stream)
- Raises:
-ValueError – If the dxtype is not a valid type, ValueError is
+
ValueError – If the dxtype is not a valid type, ValueError is
raised.
@@ -508,8 +506,8 @@ Classes and functions
- Parameters:
-id (str) – arbitrary string
components (dict) –
dictionary of DXclass instances (no sanity check on the
+
id (str) – arbitrary string
components (dict) –
dictionary of DXclass instances (no sanity check on the
individual ids!) which correspond to
positions
Classes and functionsdata
-comments (list) – list of strings; each string becomes a comment line
+
comments (list) – list of strings; each string becomes a comment line
prefixed with ‘#’. Avoid newlines.
Classes and functions
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/formats/gOpenMol.html b/gridData/formats/gOpenMol.html
index e24063f..7d71c7b 100644
--- a/gridData/formats/gOpenMol.html
+++ b/gridData/formats/gOpenMol.html
@@ -14,30 +14,28 @@
+
+
- gOpenMol — the gOpenMol plt format — GridDataFormats 1.0.2+7.g020b199 documentation
+ gOpenMol — the gOpenMol plt format — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -157,7 +155,7 @@
The module provides a simple implementation of a reader for gOpenMol
plt files. Plt files are binary files. The Plt reader tries
to guess the endianess of the file, but this can fail (with a
-TypeError); you are on your own in this case.
+TypeError); you are on your own in this case.
Only the reader is implemented. If you want to write gridded data use a format
that is more standard, such as OpenDX (see OpenDX).
@@ -347,7 +345,7 @@ Classes
aria-label="versions">
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/formats/mrc.html b/gridData/formats/mrc.html
index c1fa08e..6e13b5e 100644
--- a/gridData/formats/mrc.html
+++ b/gridData/formats/mrc.html
@@ -14,30 +14,28 @@
+
+
- mrc — the MRC/CCP4 volumetric data format — GridDataFormats 1.0.2+7.g020b199 documentation
+ mrc — the MRC/CCP4 volumetric data format — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -158,7 +156,7 @@
mrc — the MRC/CCP4 volumetric data format
-New in version 0.7.0.
+Added in version 0.7.0.
Reading of MRC/CCP4 volumetric files (MRC2014 file format) using
the mrcfile library [Burnley2017].
@@ -183,10 +181,10 @@ Classes
the mrcfile library.
- Parameters:
-filename (str (optional)) – input file (or stream), can be compressed
+filename (str (optional)) – input file (or stream), can be compressed
- Raises:
-ValueError – If the unit cell is not orthorhombic or if the data
+
ValueError – If the unit cell is not orthorhombic or if the data
are not volumetric.
@@ -196,7 +194,7 @@ Classes
Header data from the MRC file as a numpy record array.
- Type:
--
+
-
Classes
regardless of the order in the mrc file.
- Type:
--
+
-
Classes
(taken from the mrcfile.mrcfile.voxel_size attribute)
- Type:
--
+
-
Classes
header.origin.nzstart and the spacing delta)
- Type:
--
+
-
@@ -246,7 +244,7 @@ Classes
The integer 3, denoting that only 3D maps are read.
Classes
Notes
Only volumetric (3D) densities are read.
Only orthorhombic unitcells supported (other raise ValueError)
Only orthorhombic unitcells supported (other raise ValueError)
Only reading is currently supported.
-New in version 0.7.0.
+Added in version 0.7.0.
-
@@ -325,7 +323,7 @@
Classes
aria-label="versions">
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/gridData/overview.html b/gridData/overview.html
index 13737e3..d400d51 100644
--- a/gridData/overview.html
+++ b/gridData/overview.html
@@ -14,30 +14,28 @@
+
+
- Handling grids of data — gridData — GridDataFormats 1.0.2+7.g020b199 documentation
+ Handling grids of data — gridData — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -142,7 +140,7 @@ Overview
The Grid object can be resampled at arbitrary
resolution (by interpolating the data). Standard algebraic operations
are defined for grids on a point-wise basis (same as for
-numpy.ndarray).
+numpy.ndarray).
Description
@@ -163,17 +161,17 @@ DescriptionGrid objects have some convenient properties:
-The data is represented as a numpy.ndarray in
+
The data is represented as a numpy.ndarray in
Grid.grid and thus can be directly
manipulated with all the tools available in NumPy.
Grid instances can be manipulated arithmetically, e.g. one
can simply add or subtract two of them and get another one, or
multiply by a constant. Note that all operations are defined
-point-wise (see the numpy documentation for details) and that
+point-wise (see the numpy documentation for details) and that
only grids defined on the same cell edges can be combined.
A Grid object can also be created from
within python code e.g. from the output of the
-numpy.histogramdd() function.
numpy.histogramdd() function.
The representation of the data is abstracted from the format that
the files are saved in. This makes it straightforward to add
additional readers for new formats.
Formats
aria-label="versions">
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/index.html b/index.html
index 00b1fba..b13c02f 100644
--- a/index.html
+++ b/index.html
@@ -14,30 +14,29 @@
+
+
- GridDataFormats: Handling volumetric data in Python — GridDataFormats 1.0.2+7.g020b199 documentation
+ GridDataFormats: Handling volumetric data in Python — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
@@ -124,10 +123,10 @@
GridDataFormats: Handling volumetric data in Python
- Release:
-1.0.2+7.g020b199
+1.0.2+8.g86a4109
- Date:
-Jan 22, 2024
+Nov 11, 2024
- Citation:
@@ -192,7 +191,7 @@ GridDataFormats: Handling volumetric data in Python
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/installation.html b/installation.html
index d904810..2351104 100644
--- a/installation.html
+++ b/installation.html
@@ -14,30 +14,28 @@
+
+
- Installation — GridDataFormats 1.0.2+7.g020b199 documentation
+ Installation — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -211,7 +209,7 @@ Installation
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/py-modindex.html b/py-modindex.html
index 2a559d1..f118126 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -14,29 +14,27 @@
+
+
- Python Module Index — GridDataFormats 1.0.2+7.g020b199 documentation
+ Python Module Index — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -194,7 +192,7 @@ Python Module Index
aria-label="versions">
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/search.html b/search.html
index e563234..1d7490e 100644
--- a/search.html
+++ b/search.html
@@ -14,30 +14,28 @@
+
+
- Search — GridDataFormats 1.0.2+7.g020b199 documentation
+ Search — GridDataFormats 1.0.2+8.g86a4109 documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -167,7 +165,7 @@
aria-label="versions">
- 1.0.2+7.g020b199
+ 1.0.2+8.g86a4109
diff --git a/searchindex.js b/searchindex.js
index 720876f..13cb6f3 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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