Files
Jungfraujoch/PIXEL_MASK.html
T
2026-10-06 20:38:39 +00:00

13 lines
20 KiB
HTML
Raw Blame History

This file contains ambiguous Unicode characters
This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.
<!DOCTYPE html> <html lang=en data-content_root="./"> <meta charset=utf-8 /> <meta name=viewport content="width=device-width, initial-scale=1.0" /><meta name=viewport content="width=device-width, initial-scale=1" /> <meta name=viewport content="width=device-width,initial-scale=1"> <meta http-equiv=x-ua-compatible content="ie=edge"> <meta name="lang:clipboard.copy" content="Copy to clipboard"> <meta name="lang:clipboard.copied" content="Copied to clipboard"> <meta name="lang:search.language" content=en > <meta name="lang:search.pipeline.stopwords" content=True > <meta name="lang:search.pipeline.trimmer" content=True > <meta name="lang:search.result.none" content="No matching documents"> <meta name="lang:search.result.one" content="1 matching document"> <meta name="lang:search.result.other" content="# matching documents"> <meta name="lang:search.tokenizer" content="[\s\-]+"> <link href="https://fonts.gstatic.com/" rel=preconnect crossorigin> <link href="https://fonts.googleapis.com/css?family=Roboto+Mono:400,500,700|Roboto:300,400,400i,700&display=fallback" rel=stylesheet > <style> body, input { font-family: "Roboto", "Helvetica Neue", Helvetica, Arial, sans-serif } code, kbd, pre { font-family: "Roboto Mono", "Courier New", Courier, monospace } </style> <link rel=stylesheet href="_static/stylesheets/application.css"/> <link rel=stylesheet href="_static/stylesheets/application-palette.css"/> <link rel=stylesheet href="_static/stylesheets/application-fixes.css"/> <link rel=stylesheet href="_static/fonts/material-icons.css"/> <meta name=theme-color content="#3f51b5"> <script src="_static/javascripts/modernizr.js"></script> <title>Pixel mask &#8212; Jungfraujoch 1.0.0-rc.174 documentation</title> <link rel=stylesheet type="text/css" href="_static/pygments.css?v=83e35b93" /> <link rel=stylesheet type="text/css" href="_static/material.css?v=79c92029" /> <script src="_static/documentation_options.js?v=3dccfb20"></script> <script src="_static/doctools.js?v=9bcbadda"></script> <script src="_static/sphinx_highlight.js?v=dc90522c"></script> <link rel=icon href="_static/jfjoch.png"/> <link rel=index title=Index href=genindex.html /> <link rel=search title=Search href=search.html /> <link rel=next title="Web frontend" href=WEB_FRONTEND.html /> <link rel=prev title="Data streams" href=IMAGE_STREAM.html /> <body dir=ltr data-md-color-primary=indigo data-md-color-accent=lime> <svg class=md-svg > <defs data-children-count=0 > <svg xmlns="http://www.w3.org/2000/svg" width=500 height=500 viewBox="0 0 500 500" id=__gitlab ><path fill=currentColor d="M93.667 473.347l90.684-279.097H2.983l90.684 279.097z" transform="translate(156.198 1.16)"/><path fill=currentColor d="M221.333 473.345L130.649 194.25H3.557l217.776 279.095z" transform="translate(28.531 1.16)" opacity=.7 /><path fill=currentColor d="M32 195.155L4.441 279.97a18.773 18.773 0 0 0 6.821 20.99l238.514 173.29L32 195.155z" transform="translate(.089 .256)" opacity=.5 /><path fill=currentColor d="M2.667-84.844h127.092L75.14-252.942c-2.811-8.649-15.047-8.649-17.856 0L2.667-84.844z" transform="translate(29.422 280.256)"/><path fill=currentColor d="M2.667 473.345L93.351 194.25h127.092L2.667 473.345z" transform="translate(247.198 1.16)" opacity=.7 /><path fill=currentColor d="M221.334 195.155l27.559 84.815a18.772 18.772 0 0 1-6.821 20.99L3.557 474.25l217.777-279.095z" transform="translate(246.307 .256)" opacity=.5 /><path fill=currentColor d="M130.667-84.844H3.575l54.618-168.098c2.811-8.649 15.047-8.649 17.856 0l54.618 168.098z" transform="translate(336.974 280.256)"/></svg> </defs> </svg> <input class=md-toggle data-md-toggle=drawer type=checkbox id=__drawer > <input class=md-toggle data-md-toggle=search type=checkbox id=__search > <label class=md-overlay data-md-component=overlay for=__drawer ></label> <a href="#PIXEL_MASK" tabindex=1 class=md-skip > Skip to content </a> <header class=md-header data-md-component=header > <nav class="md-header-nav md-grid"> <div class="md-flex navheader"> <div class="md-flex__cell md-flex__cell--shrink"> <a href=index.html title="Jungfraujoch 1.0.0-rc.174 documentation" class="md-header-nav__button md-logo"> <i class=md-icon >&#xe30d</i> </a> </div> <div class="md-flex__cell md-flex__cell--shrink"> <label class="md-icon md-icon--menu md-header-nav__button" for=__drawer ></label> </div> <div class="md-flex__cell md-flex__cell--stretch"> <div class="md-flex__ellipsis md-header-nav__title" data-md-component=title > <span class=md-header-nav__topic >PSI Jungfraujoch</span> <span class=md-header-nav__topic > Pixel mask </span> </div> </div> <div class="md-flex__cell md-flex__cell--shrink"> <label class="md-icon md-icon--search md-header-nav__button" for=__search ></label> <div class=md-search data-md-component=search role=dialog > <label class=md-search__overlay for=__search ></label> <div class=md-search__inner role=search > <form class=md-search__form action=search.html method=get name=search > <input type=text class=md-search__input name=q placeholder=""Search"" autocapitalize=off autocomplete=off spellcheck=false data-md-component=query data-md-state=active > <label class="md-icon md-search__icon" for=__search ></label> <button type=reset class="md-icon md-search__icon" data-md-component=reset tabindex=-1 > &#xE5CD; </button> </form> <div class=md-search__output > <div class=md-search__scrollwrap data-md-scrollfix> <div class=md-search-result data-md-component=result > <div class=md-search-result__meta > Type to start searching </div> <ol class=md-search-result__list ></ol> </div> </div> </div> </div> </div> </div> <div class="md-flex__cell md-flex__cell--shrink"> <div class=md-header-nav__source > <a href="https://gitea.psi.ch/mx/jungfraujoch" title="Go to repository" class=md-source data-md-source=github > <div class=md-source__icon > <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 24 24" width=28 height=28 > <use xlink:href="#__gitlab" width=24 height=24 ></use> </svg> </div> <div class=md-source__repository > Jungfraujoch </div> </a> </div> </div> <script src="_static/javascripts/version_dropdown.js"></script> <script> var json_loc = ""versions.json"", target_loc = "../", text = "Versions"; $( document ).ready( add_version_dropdown(json_loc, target_loc, text)); </script> </div> </nav> </header> <div class=md-container > <nav class=md-tabs data-md-component=tabs > <div class="md-tabs__inner md-grid"> <ul class=md-tabs__list > <li class=md-tabs__item ><a href=index.html class=md-tabs__link >Jungfraujoch 1.0.0-rc.174 documentation</a> </ul> </div> </nav> <main class=md-main > <div class="md-main__inner md-grid" data-md-component=container > <div class="md-sidebar md-sidebar--primary" data-md-component=navigation > <div class=md-sidebar__scrollwrap > <div class=md-sidebar__inner > <nav class="md-nav md-nav--primary" data-md-level=0 > <label class="md-nav__title md-nav__title--site" for=__drawer > <a href=index.html title="Jungfraujoch 1.0.0-rc.174 documentation" class="md-nav__button md-logo"> <i class=md-icon >&#xe30d</i> </a> <a href=index.html title="Jungfraujoch 1.0.0-rc.174 documentation">PSI Jungfraujoch</a> </label> <div class=md-nav__source > <a href="https://gitea.psi.ch/mx/jungfraujoch" title="Go to repository" class=md-source data-md-source=github > <div class=md-source__icon > <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 24 24" width=28 height=28 > <use xlink:href="#__gitlab" width=24 height=24 ></use> </svg> </div> <div class=md-source__repository > Jungfraujoch </div> </a> </div> <ul class=md-nav__list > <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >rugnux — data processing</span></span> <li class=md-nav__item > <a href=RUGNUX.html class=md-nav__link >Rugnux</a> <li class=md-nav__item > <a href=RUGNUX_OVERVIEW.html class=md-nav__link >What Rugnux does</a> <li class=md-nav__item > <a href=RUGNUX_INSTALL.html class=md-nav__link >Installing Rugnux</a> <li class=md-nav__item > <a href=RUGNUX_FORMATS.html class=md-nav__link >What Rugnux reads</a> <li class=md-nav__item > <a href=RUGNUX_TUTORIAL.html class=md-nav__link >Running Rugnux</a> <li class=md-nav__item > <a href=RUGNUX_INTEGRATION.html class=md-nav__link >Rugnux with other programs</a> <li class=md-nav__item > <a href=RUGNUX_REPORT.html class=md-nav__link >The results report</a> <li class=md-nav__item > <a href=RUGNUX_ADVANCED.html class=md-nav__link >Advanced Rugnux</a> <li class=md-nav__item > <a href=RUGNUX_CALIBRATION.html class=md-nav__link >Detector calibration from powder rings (<code class="docutils literal notranslate"><span class=pre >rugnux</span> <span class=pre >--mode</span> <span class=pre >calibration</span></code>)</a> <li class=md-nav__item > <a href=CPU_DATA_ANALYSIS.html class=md-nav__link >CPU-side crystallographic data analysis (Jungfraujoch)</a> <li class=md-nav__item > <a href=CPU_DATA_ANALYSIS_IMAGE.html class=md-nav__link >Data analysis: from images to spots (§0–§3)</a> <li class=md-nav__item > <a href=CPU_DATA_ANALYSIS_INDEXING.html class=md-nav__link >Data analysis: indexing and geometry (§4–§7)</a> <li class=md-nav__item > <a href=CPU_DATA_ANALYSIS_INTEGRATION.html class=md-nav__link >Data analysis: integration, scaling and merging (§8–§12)</a> <li class=md-nav__item > <a href=CPU_DATA_ANALYSIS_DECISIONS.html class=md-nav__link >Data analysis: space group and validation (§13–§14)</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Jungfraujoch — acquisition</span></span> <li class=md-nav__item > <a href=JFJOCH_BROKER.html class=md-nav__link >jfjoch_broker</a> <li class=md-nav__item > <a href=JFJOCH_WRITER.html class=md-nav__link >jfjoch_writer</a> <li class=md-nav__item > <a href=JFJOCH_VIEWER.html class=md-nav__link >jfjoch_viewer</a> <li class=md-nav__item > <a href=SOFTWARE_INTEGRATION.html class=md-nav__link >Integration with MX data processing software</a> <li class=md-nav__item > <a href=TOOLS.html class=md-nav__link >Tools</a> <li class=md-nav__item > <a href=DEPLOYMENT.html class=md-nav__link >Deployment</a> <li class=md-nav__item > <a href=DETECTORS.html class=md-nav__link >Supported detectors</a> <li class=md-nav__item > <a href=HARDWARE.html class=md-nav__link >Hardware requirements</a> <li class=md-nav__item > <a href=SOFTWARE.html class=md-nav__link >Software requirements</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >FPGA</span></span> <li class=md-nav__item > <a href=FPGA.html class=md-nav__link >FPGA smartNIC</a> <li class=md-nav__item > <a href=FPGA_LICENSE.html class=md-nav__link >FPGA license</a> <li class=md-nav__item > <a href=FPGA_DESIGN.html class=md-nav__link >FPGA data flow</a> <li class=md-nav__item > <a href=FPGA_NETWORK.html class=md-nav__link >FPGA network</a> <li class=md-nav__item > <a href=FPGA_PCIE_DRIVER.html class=md-nav__link >FPGA PCIe driver</a> <li class=md-nav__item > <a href=FPGA_SETTINGS.html class=md-nav__link >FPGA advanced reference</a> <li class=md-nav__item > <a href=FPGA_DATA_ANALYSIS.html class=md-nav__link >FPGA data analysis</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Reference</span></span> <li class=md-nav__item > <a href=DETECTOR_GEOMETRY.html class=md-nav__link >Detector geometry</a> <li class=md-nav__item > <a href=OPENAPI.html class=md-nav__link >OpenAPI</a> <li class=md-nav__item > <a href=OPENAPI_SPECS.html class=md-nav__link >OpenAPI specification</a> <li class=md-nav__item > <a href=PYTHON_CLIENT.html class=md-nav__link >OpenAPI Python client</a> <li class=md-nav__item > <a href=CBOR.html class=md-nav__link >CBOR messages</a> <li class=md-nav__item > <a href=HDF5.html class=md-nav__link >HDF5 / NeXus data format</a> <li class=md-nav__item > <a href=IMAGE_STREAM.html class=md-nav__link >Data streams</a> <li class=md-nav__item > <input class="md-toggle md-nav__toggle" data-md-toggle=toc type=checkbox id=__toc > <label class="md-nav__link md-nav__link--active" for=__toc > Pixel mask </label> <a href="#" class="md-nav__link md-nav__link--active">Pixel mask</a> <nav class="md-nav md-nav--secondary"> <ul class=md-nav__list data-md-scrollfix=""> </ul> </nav> <ul class=md-nav__list > <li class=md-nav__item > <a href="#mask-format" class=md-nav__link >Mask format</a> <li class=md-nav__item > <a href="#custom-user-mask" class=md-nav__link >Custom user mask</a> </ul> <li class=md-nav__item > <a href=WEB_FRONTEND.html class=md-nav__link >Web frontend</a> <li class=md-nav__item > <a href=TESTS.html class=md-nav__link >Tests</a> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Project</span></span> <li class=md-nav__item > <a href=ACKNOWLEDGEMENT.html class=md-nav__link >Acknowledgements</a> <li class=md-nav__item > <a href=EXTERNAL_TEST_DATA.html class=md-nav__link >External test data</a> <li class=md-nav__item > <a href=LICENSE.html class=md-nav__link >License</a> <li class=md-nav__item > <a href=THIRD_PARTY_NOTICES.html class=md-nav__link >Third-party software notices</a> <li class=md-nav__item > <a href=VERSIONING.html class=md-nav__link >Semantic versioning</a> <li class=md-nav__item > <a href=SECURITY.html class=md-nav__link >Security</a> <li class=md-nav__item > <a href=RELEASE_CONTENTS.html class=md-nav__link >Release contents</a> <li class=md-nav__item > <a href=REPOSITORIES.html class=md-nav__link >Linux package repositories</a> <li class=md-nav__item > <a href=NAMING.html class=md-nav__link >Naming</a> <li class=md-nav__item > <a href=CHANGELOG.html class=md-nav__link >Changelog</a> </ul> </nav> </div> </div> </div> <div class="md-sidebar md-sidebar--secondary" data-md-component=toc > <div class=md-sidebar__scrollwrap > <div class=md-sidebar__inner > <nav class="md-nav md-nav--secondary"> <ul class=md-nav__list data-md-scrollfix=""> </ul> </nav> </div> </div> </div> <div class=md-content > <article class="md-content__inner md-typeset" role=main > <section class="tex2jax_ignore mathjax_ignore" id=pixel-mask > <h1 id=pixel-mask--page-root >Pixel mask<a class=headerlink href="#pixel-mask--page-root" title="Link to this heading"></a></h1> <section id=mask-format > <h2 id=mask-format >Mask format<a class=headerlink href="#mask-format" title="Link to this heading"></a></h2> <p>Jungfraujoch generally follows the <a class="reference external" href="https://manual.nexusformat.org/classes/applications/NXmx.html">NXmx format</a> for the pixel mask. The pixel mask is a 32-bit unsigned integer array of the same size as the image. The conditions for masking a pixel are encoded by setting a particular bit to one. This makes it possible to record the reason why a pixel is included in the mask, and several reasons can be recorded for one pixel at the same time.</p> <p>Bit values are set as follows:</p> <p>Bit 0 - gap (pixel with no sensor)</p> <p>Bit 1 - error pixel (for PSI JUNGFRAU: pixel doesn’t set proper gain during pedestal, for DECTRIS: pixel is part of detector pixel mask)</p> <p>Bit 4 - noisy pixel (for PSI JUNGFRAU: pixel pedestal G0 RMS is over threshold, for DECTRIS: pixel was flagged with signal during dark data collection at initialization)</p> <p>Bit 8 - user defined mask</p> <p>Bit 9 - beam stop shadow (found by <code class="docutils literal notranslate"><span class=pre >rugnux</span> <span class=pre >--detect-beam-stop</span></code>, on by default; see <a class="reference internal" href=RUGNUX.html ><span class="std std-doc">Rugnux</span></a>). Unlike the other bits this one belongs to the run that found it, not to the dataset: Rugnux clears it at the start of every run, so a mask read back from a file that carries one starts clear. The user mask (bit 8) is left alone.</p> <p>Bit 10 - defective pixel found on the run’s own frames (rotation data from a counting sensor; see <a class="reference internal" href=CPU_DATA_ANALYSIS_IMAGE.html ><span class="std std-doc">CPU data analysis §1.6</span></a>): lit above its resolution ring on more frames than one reflection or chance explains, or holding the detector’s error value on most frames.</p> <p>Bit 30 - module edge (only for PSI systems)</p> <p>Bit 31 - chip edge interpolated pixel (multipixel)</p> </section> <section id=custom-user-mask > <h2 id=custom-user-mask >Custom user mask<a class=headerlink href="#custom-user-mask" title="Link to this heading"></a></h2> <p>Jungfraujoch allows a custom user mask to be uploaded. This happens in two steps. First create the mask in TIFF format:</p> <div class="highlight-python notranslate"><div class=highlight ><pre><span></span><span class=kn >import</span> <span class=nn >numpy</span> <span class=k >as</span> <span class=nn >np</span>
<span class=kn >import</span> <span class=nn >tifffile</span> <span class=k >as</span> <span class=nn >tiff</span>
<span class=c1 ># Create an array matching a 2068 x 2164 (width x height) image: 2164 rows, 2068 columns</span>
<span class=n >array</span> <span class=o >=</span> <span class=n >np</span><span class=o >.</span><span class=n >zeros</span><span class=p >((</span><span class=mi >2164</span><span class=p >,</span> <span class=mi >2068</span><span class=p >),</span> <span class=n >dtype</span><span class=o >=</span><span class=n >np</span><span class=o >.</span><span class=n >uint32</span><span class=p >)</span>
<span class=c1 ># Mark the pixel at column 400, row 300 with the value 1</span>
<span class=n >array</span><span class=p >[</span><span class=mi >300</span><span class=p >,</span> <span class=mi >400</span><span class=p >]</span> <span class=o >=</span> <span class=mi >1</span>
<span class=c1 ># Save the array as a TIFF file</span>
<span class=n >tiff</span><span class=o >.</span><span class=n >imwrite</span><span class=p >(</span><span class=s1 >'mask.tiff'</span><span class=p >,</span> <span class=n >array</span><span class=p >)</span>
</pre></div> </div> <p>Pixels with non-zero value in the TIFF file will be marked as belonging to the user mask (bit 8).</p> <p>Then upload the mask to Jungfraujoch server:</p> <div class="highlight-shell notranslate"><div class=highlight ><pre><span></span>curl<span class=w > </span>-v<span class=w > </span>http://&lt;jfjoch_broker<span class=w > </span>http<span class=w > </span>address&gt;/config/user_mask.tiff<span class=w > </span>-XPUT<span class=w > </span>--data-binary<span class=w > </span>@mask.tiff
</pre></div> </div> </section> </section> </article> </div> </div> </main> </div> <footer class=md-footer > <div class=md-footer-nav > <nav class="md-footer-nav__inner md-grid"> <a href=IMAGE_STREAM.html title="Data streams" class="md-flex md-footer-nav__link md-footer-nav__link--prev" rel=prev > <div class="md-flex__cell md-flex__cell--shrink"> <i class="md-icon md-icon--arrow-back md-footer-nav__button"></i> </div> <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"> <span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Previous" </span> Data streams </span> </div> </a> <a href=WEB_FRONTEND.html title="Web frontend" class="md-flex md-footer-nav__link md-footer-nav__link--next" rel=next > <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"><span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Next" </span> Web frontend </span> </div> <div class="md-flex__cell md-flex__cell--shrink"><i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i> </div> </a> </nav> </div> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-footer-copyright > <div class=md-footer-copyright__highlight > &#169; Copyright 2024, Paul Scherrer Institute. </div> Created using <a href="http://www.sphinx-doc.org/">Sphinx</a> 8.1.3. and <a href="https://github.com/bashtage/sphinx-material/">Material for Sphinx</a> </div> </div> </div> </footer> <script src="_static/javascripts/application.js"></script> <script>app.initialize({version: "1.0.4", url: {base: ".."}})</script>