A loose federation of distributed, typed datasets
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401
402 <ul>
403 <li><a href="#atdata.SampleBatch" id="toc-atdata.SampleBatch" class="nav-link active" data-scroll-target="#atdata.SampleBatch">SampleBatch</a>
404 <ul class="collapse">
405 <li><a href="#parameters" id="toc-parameters" class="nav-link" data-scroll-target="#parameters">Parameters</a></li>
406 <li><a href="#attributes" id="toc-attributes" class="nav-link" data-scroll-target="#attributes">Attributes</a></li>
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419
420<section id="atdata.SampleBatch" class="level1">
421<h1>SampleBatch</h1>
422<div class="sourceCode" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>SampleBatch(samples)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
423<p>A batch of samples with automatic attribute aggregation.</p>
424<p>This class wraps a sequence of samples and provides magic <code>__getattr__</code> access to aggregate sample attributes. When you access an attribute that exists on the sample type, it automatically aggregates values across all samples in the batch.</p>
425<p>NDArray fields are stacked into a numpy array with a batch dimension. Other fields are aggregated into a list.</p>
426<section id="parameters" class="level2 doc-section doc-section-parameters">
427<h2 class="doc-section doc-section-parameters anchored" data-anchor-id="parameters">Parameters</h2>
428<table class="caption-top table">
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431<col style="width: 9%">
432<col style="width: 66%">
433<col style="width: 14%">
434</colgroup>
435<thead>
436<tr class="header">
437<th>Name</th>
438<th>Type</th>
439<th>Description</th>
440<th>Default</th>
441</tr>
442</thead>
443<tbody>
444<tr class="odd">
445<td>DT</td>
446<td></td>
447<td>The sample type, must derive from <code>PackableSample</code>.</td>
448<td><em>required</em></td>
449</tr>
450</tbody>
451</table>
452</section>
453<section id="attributes" class="level2 doc-section doc-section-attributes">
454<h2 class="doc-section doc-section-attributes anchored" data-anchor-id="attributes">Attributes</h2>
455<table class="caption-top table">
456<thead>
457<tr class="header">
458<th>Name</th>
459<th>Type</th>
460<th>Description</th>
461</tr>
462</thead>
463<tbody>
464<tr class="odd">
465<td>samples</td>
466<td></td>
467<td>The list of sample instances in this batch.</td>
468</tr>
469</tbody>
470</table>
471</section>
472<section id="examples" class="level2 doc-section doc-section-examples">
473<h2 class="doc-section doc-section-examples anchored" data-anchor-id="examples">Examples</h2>
474<div class="sourceCode" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> batch <span class="op">=</span> SampleBatch[MyData]([sample1, sample2, sample3])</span>
475<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> batch.embeddings <span class="co"># Returns stacked numpy array of shape (3, ...)</span></span>
476<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> batch.names <span class="co"># Returns list of names</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
477</section>
478<section id="note" class="level2 doc-section doc-section-note">
479<h2 class="doc-section doc-section-note anchored" data-anchor-id="note">Note</h2>
480<p>This class uses Python’s <code>__orig_class__</code> mechanism to extract the type parameter at runtime. Instances must be created using the subscripted syntax <code>SampleBatch[MyType](samples)</code> rather than calling the constructor directly with an unsubscripted class.</p>
481
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550 const getTextToCopy = function(trigger) {
551 const codeEl = trigger.previousElementSibling.cloneNode(true);
552 for (const childEl of codeEl.children) {
553 if (isCodeAnnotation(childEl)) {
554 childEl.remove();
555 }
556 }
557 return codeEl.innerText;
558 }
559 const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
560 text: getTextToCopy
561 });
562 clipboard.on('success', onCopySuccess);
563 if (window.document.getElementById('quarto-embedded-source-code-modal')) {
564 const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
565 text: getTextToCopy,
566 container: window.document.getElementById('quarto-embedded-source-code-modal')
567 });
568 clipboardModal.on('success', onCopySuccess);
569 }
570 var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
571 var mailtoRegex = new RegExp(/^mailto:/);
572 var filterRegex = new RegExp("https:\/\/github\.com\/your-org\/atdata");
573 var isInternal = (href) => {
574 return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
575 }
576 // Inspect non-navigation links and adorn them if external
577 var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
578 for (var i=0; i<links.length; i++) {
579 const link = links[i];
580 if (!isInternal(link.href)) {
581 // undo the damage that might have been done by quarto-nav.js in the case of
582 // links that we want to consider external
583 if (link.dataset.originalHref !== undefined) {
584 link.href = link.dataset.originalHref;
585 }
586 }
587 }
588 function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
589 const config = {
590 allowHTML: true,
591 maxWidth: 500,
592 delay: 100,
593 arrow: false,
594 appendTo: function(el) {
595 return el.parentElement;
596 },
597 interactive: true,
598 interactiveBorder: 10,
599 theme: 'quarto',
600 placement: 'bottom-start',
601 };
602 if (contentFn) {
603 config.content = contentFn;
604 }
605 if (onTriggerFn) {
606 config.onTrigger = onTriggerFn;
607 }
608 if (onUntriggerFn) {
609 config.onUntrigger = onUntriggerFn;
610 }
611 window.tippy(el, config);
612 }
613 const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
614 for (var i=0; i<noterefs.length; i++) {
615 const ref = noterefs[i];
616 tippyHover(ref, function() {
617 // use id or data attribute instead here
618 let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
619 try { href = new URL(href).hash; } catch {}
620 const id = href.replace(/^#\/?/, "");
621 const note = window.document.getElementById(id);
622 if (note) {
623 return note.innerHTML;
624 } else {
625 return "";
626 }
627 });
628 }
629 const xrefs = window.document.querySelectorAll('a.quarto-xref');
630 const processXRef = (id, note) => {
631 // Strip column container classes
632 const stripColumnClz = (el) => {
633 el.classList.remove("page-full", "page-columns");
634 if (el.children) {
635 for (const child of el.children) {
636 stripColumnClz(child);
637 }
638 }
639 }
640 stripColumnClz(note)
641 if (id === null || id.startsWith('sec-')) {
642 // Special case sections, only their first couple elements
643 const container = document.createElement("div");
644 if (note.children && note.children.length > 2) {
645 container.appendChild(note.children[0].cloneNode(true));
646 for (let i = 1; i < note.children.length; i++) {
647 const child = note.children[i];
648 if (child.tagName === "P" && child.innerText === "") {
649 continue;
650 } else {
651 container.appendChild(child.cloneNode(true));
652 break;
653 }
654 }
655 if (window.Quarto?.typesetMath) {
656 window.Quarto.typesetMath(container);
657 }
658 return container.innerHTML
659 } else {
660 if (window.Quarto?.typesetMath) {
661 window.Quarto.typesetMath(note);
662 }
663 return note.innerHTML;
664 }
665 } else {
666 // Remove any anchor links if they are present
667 const anchorLink = note.querySelector('a.anchorjs-link');
668 if (anchorLink) {
669 anchorLink.remove();
670 }
671 if (window.Quarto?.typesetMath) {
672 window.Quarto.typesetMath(note);
673 }
674 if (note.classList.contains("callout")) {
675 return note.outerHTML;
676 } else {
677 return note.innerHTML;
678 }
679 }
680 }
681 for (var i=0; i<xrefs.length; i++) {
682 const xref = xrefs[i];
683 tippyHover(xref, undefined, function(instance) {
684 instance.disable();
685 let url = xref.getAttribute('href');
686 let hash = undefined;
687 if (url.startsWith('#')) {
688 hash = url;
689 } else {
690 try { hash = new URL(url).hash; } catch {}
691 }
692 if (hash) {
693 const id = hash.replace(/^#\/?/, "");
694 const note = window.document.getElementById(id);
695 if (note !== null) {
696 try {
697 const html = processXRef(id, note.cloneNode(true));
698 instance.setContent(html);
699 } finally {
700 instance.enable();
701 instance.show();
702 }
703 } else {
704 // See if we can fetch this
705 fetch(url.split('#')[0])
706 .then(res => res.text())
707 .then(html => {
708 const parser = new DOMParser();
709 const htmlDoc = parser.parseFromString(html, "text/html");
710 const note = htmlDoc.getElementById(id);
711 if (note !== null) {
712 const html = processXRef(id, note);
713 instance.setContent(html);
714 }
715 }).finally(() => {
716 instance.enable();
717 instance.show();
718 });
719 }
720 } else {
721 // See if we can fetch a full url (with no hash to target)
722 // This is a special case and we should probably do some content thinning / targeting
723 fetch(url)
724 .then(res => res.text())
725 .then(html => {
726 const parser = new DOMParser();
727 const htmlDoc = parser.parseFromString(html, "text/html");
728 const note = htmlDoc.querySelector('main.content');
729 if (note !== null) {
730 // This should only happen for chapter cross references
731 // (since there is no id in the URL)
732 // remove the first header
733 if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
734 note.children[0].remove();
735 }
736 const html = processXRef(null, note);
737 instance.setContent(html);
738 }
739 }).finally(() => {
740 instance.enable();
741 instance.show();
742 });
743 }
744 }, function(instance) {
745 });
746 }
747 let selectedAnnoteEl;
748 const selectorForAnnotation = ( cell, annotation) => {
749 let cellAttr = 'data-code-cell="' + cell + '"';
750 let lineAttr = 'data-code-annotation="' + annotation + '"';
751 const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
752 return selector;
753 }
754 const selectCodeLines = (annoteEl) => {
755 const doc = window.document;
756 const targetCell = annoteEl.getAttribute("data-target-cell");
757 const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
758 const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
759 const lines = annoteSpan.getAttribute("data-code-lines").split(",");
760 const lineIds = lines.map((line) => {
761 return targetCell + "-" + line;
762 })
763 let top = null;
764 let height = null;
765 let parent = null;
766 if (lineIds.length > 0) {
767 //compute the position of the single el (top and bottom and make a div)
768 const el = window.document.getElementById(lineIds[0]);
769 top = el.offsetTop;
770 height = el.offsetHeight;
771 parent = el.parentElement.parentElement;
772 if (lineIds.length > 1) {
773 const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
774 const bottom = lastEl.offsetTop + lastEl.offsetHeight;
775 height = bottom - top;
776 }
777 if (top !== null && height !== null && parent !== null) {
778 // cook up a div (if necessary) and position it
779 let div = window.document.getElementById("code-annotation-line-highlight");
780 if (div === null) {
781 div = window.document.createElement("div");
782 div.setAttribute("id", "code-annotation-line-highlight");
783 div.style.position = 'absolute';
784 parent.appendChild(div);
785 }
786 div.style.top = top - 2 + "px";
787 div.style.height = height + 4 + "px";
788 div.style.left = 0;
789 let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
790 if (gutterDiv === null) {
791 gutterDiv = window.document.createElement("div");
792 gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
793 gutterDiv.style.position = 'absolute';
794 const codeCell = window.document.getElementById(targetCell);
795 const gutter = codeCell.querySelector('.code-annotation-gutter');
796 gutter.appendChild(gutterDiv);
797 }
798 gutterDiv.style.top = top - 2 + "px";
799 gutterDiv.style.height = height + 4 + "px";
800 }
801 selectedAnnoteEl = annoteEl;
802 }
803 };
804 const unselectCodeLines = () => {
805 const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
806 elementsIds.forEach((elId) => {
807 const div = window.document.getElementById(elId);
808 if (div) {
809 div.remove();
810 }
811 });
812 selectedAnnoteEl = undefined;
813 };
814 // Handle positioning of the toggle
815 window.addEventListener(
816 "resize",
817 throttle(() => {
818 elRect = undefined;
819 if (selectedAnnoteEl) {
820 selectCodeLines(selectedAnnoteEl);
821 }
822 }, 10)
823 );
824 function throttle(fn, ms) {
825 let throttle = false;
826 let timer;
827 return (...args) => {
828 if(!throttle) { // first call gets through
829 fn.apply(this, args);
830 throttle = true;
831 } else { // all the others get throttled
832 if(timer) clearTimeout(timer); // cancel #2
833 timer = setTimeout(() => {
834 fn.apply(this, args);
835 timer = throttle = false;
836 }, ms);
837 }
838 };
839 }
840 // Attach click handler to the DT
841 const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
842 for (const annoteDlNode of annoteDls) {
843 annoteDlNode.addEventListener('click', (event) => {
844 const clickedEl = event.target;
845 if (clickedEl !== selectedAnnoteEl) {
846 unselectCodeLines();
847 const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
848 if (activeEl) {
849 activeEl.classList.remove('code-annotation-active');
850 }
851 selectCodeLines(clickedEl);
852 clickedEl.classList.add('code-annotation-active');
853 } else {
854 // Unselect the line
855 unselectCodeLines();
856 clickedEl.classList.remove('code-annotation-active');
857 }
858 });
859 }
860 const findCites = (el) => {
861 const parentEl = el.parentElement;
862 if (parentEl) {
863 const cites = parentEl.dataset.cites;
864 if (cites) {
865 return {
866 el,
867 cites: cites.split(' ')
868 };
869 } else {
870 return findCites(el.parentElement)
871 }
872 } else {
873 return undefined;
874 }
875 };
876 var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
877 for (var i=0; i<bibliorefs.length; i++) {
878 const ref = bibliorefs[i];
879 const citeInfo = findCites(ref);
880 if (citeInfo) {
881 tippyHover(citeInfo.el, function() {
882 var popup = window.document.createElement('div');
883 citeInfo.cites.forEach(function(cite) {
884 var citeDiv = window.document.createElement('div');
885 citeDiv.classList.add('hanging-indent');
886 citeDiv.classList.add('csl-entry');
887 var biblioDiv = window.document.getElementById('ref-' + cite);
888 if (biblioDiv) {
889 citeDiv.innerHTML = biblioDiv.innerHTML;
890 }
891 popup.appendChild(citeDiv);
892 });
893 return popup.innerHTML;
894 });
895 }
896 }
897 });
898 </script>
899</div> <!-- /content -->
900<footer class="footer">
901 <div class="nav-footer">
902 <div class="nav-footer-left">
903<p>Built with <a href="https://quarto.org/">Quarto</a></p>
904</div>
905 <div class="nav-footer-center">
906
907 <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/your-org/atdata/edit/main/api/SampleBatch.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/your-org/atdata/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
908 <div class="nav-footer-right">
909<p>MIT License</p>
910</div>
911 </div>
912</footer>
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917</body></html>