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<!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>rugnux &#8212; Jungfraujoch 1.0.0-rc.161 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=010ab5da"></script> <script 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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.161 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 > rugnux </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 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<a href=index.html title="Jungfraujoch 1.0.0-rc.161 documentation" class="md-nav__button md-logo"> <i class=md-icon >&#xe30d</i> </a> <a href=index.html title="Jungfraujoch 1.0.0-rc.161 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 >General</span></span> <li class=md-nav__item > <a href=ACKNOWLEDGEMENT.html class=md-nav__link >Acknowledgements</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=DETECTORS.html class=md-nav__link >Supported detectors</a> <li class=md-nav__item > <a href="DETECTORS.html#dectris-detectors" class=md-nav__link >DECTRIS 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 > <a href=VERSIONING.html class=md-nav__link >Semantic versioning</a> <li class=md-nav__item > <a href=DEPLOYMENT.html class=md-nav__link >Deployment</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> <li class=md-nav__item > <span class="md-nav__link caption"><span class=caption-text >Software</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 > <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 > rugnux </label> <a href="#" class="md-nav__link md-nav__link--active">rugnux</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="#where-it-fits-among-the-three-analysis-tools" class=md-nav__link >Where it fits among the three analysis tools</a> <li class=md-nav__item > <a href="#hardware" class=md-nav__link >Hardware</a> <li class=md-nav__item > <a href="#input-and-output" class=md-nav__link >Input and output</a> <li class=md-nav__item > <a href="#the-results-report" class=md-nav__link >The results report</a> <li class=md-nav__item > <a href="#validating-against-a-model-rugnux-model" class=md-nav__link >Validating against a model (<code class="docutils literal notranslate"><span class=pre >rugnux</span> <span class=pre >--model</span></code>)</a> <li class=md-nav__item > <a href="#re-scaling-and-re-merging-rugnux-mode-scale" class=md-nav__link >Re-scaling and re-merging (<code class="docutils literal notranslate"><span class=pre >rugnux</span> <span class=pre >--mode</span> <span class=pre >scale</span></code>)</a> <li class=md-nav__item > <a href="#detector-calibration-from-powder-rings-rugnux-mode-calibration" 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="#quick-start" class=md-nav__link >Quick start</a> <li class=md-nav__item > <a href="#command-line-options" class=md-nav__link >Command-line options</a> </ul> <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 > <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=CPU_DATA_ANALYSIS.html class=md-nav__link >CPU-side crystallographic data analysis (Jungfraujoch)</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=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 > <a href=PIXEL_MASK.html class=md-nav__link >Pixel mask</a> <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 >OpenAPI Python client</span></span> <li class=md-nav__item > <a href="python_client/README.html" class=md-nav__link >jfjoch-client</a> <li class=md-nav__item > <a href="python_client/README.html#license-clarification" class=md-nav__link >License Clarification</a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html" class=md-nav__link >jfjoch_client.DefaultApi</a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#cancel-post" class=md-nav__link ><strong>cancel_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-azim-int-get" class=md-nav__link ><strong>config_azim_int_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-azim-int-put" class=md-nav__link ><strong>config_azim_int_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-bragg-integration-get" class=md-nav__link ><strong>config_bragg_integration_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-bragg-integration-put" class=md-nav__link ><strong>config_bragg_integration_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-dark-mask-get" class=md-nav__link ><strong>config_dark_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-dark-mask-put" class=md-nav__link ><strong>config_dark_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-detector-get" class=md-nav__link ><strong>config_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-detector-put" class=md-nav__link ><strong>config_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-file-writer-get" class=md-nav__link ><strong>config_file_writer_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-file-writer-put" class=md-nav__link ><strong>config_file_writer_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-conversion-post" class=md-nav__link ><strong>config_image_format_conversion_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-get" class=md-nav__link ><strong>config_image_format_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-put" class=md-nav__link ><strong>config_image_format_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-raw-post" class=md-nav__link ><strong>config_image_format_raw_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-indexing-get" class=md-nav__link ><strong>config_indexing_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-indexing-put" class=md-nav__link ><strong>config_indexing_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-instrument-get" class=md-nav__link ><strong>config_instrument_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-instrument-put" class=md-nav__link ><strong>config_instrument_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-internal-generator-image-put" class=md-nav__link ><strong>config_internal_generator_image_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-internal-generator-image-tiff-put" class=md-nav__link ><strong>config_internal_generator_image_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-mask-get" class=md-nav__link ><strong>config_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-mask-tiff-get" class=md-nav__link ><strong>config_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-roi-get" class=md-nav__link ><strong>config_roi_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-roi-put" class=md-nav__link ><strong>config_roi_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-get" class=md-nav__link ><strong>config_select_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-put" class=md-nav__link ><strong>config_select_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-get" class=md-nav__link ><strong>config_spot_finding_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-put" class=md-nav__link ><strong>config_spot_finding_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-get" class=md-nav__link ><strong>config_user_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-put" class=md-nav__link ><strong>config_user_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-get" class=md-nav__link ><strong>config_user_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-put" class=md-nav__link ><strong>config_user_mask_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-get" class=md-nav__link ><strong>config_zeromq_metadata_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-put" class=md-nav__link ><strong>config_zeromq_metadata_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-get" class=md-nav__link ><strong>config_zeromq_preview_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-put" class=md-nav__link ><strong>config_zeromq_preview_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#deactivate-post" class=md-nav__link ><strong>deactivate_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#detector-status-get" class=md-nav__link ><strong>detector_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#fpga-status-get" class=md-nav__link ><strong>fpga_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-clear-post" class=md-nav__link ><strong>image_buffer_clear_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-cbor-get" class=md-nav__link ><strong>image_buffer_image_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-jpeg-get" class=md-nav__link ><strong>image_buffer_image_jpeg_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-tiff-get" class=md-nav__link ><strong>image_buffer_image_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-start-cbor-get" class=md-nav__link ><strong>image_buffer_start_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-status-get" class=md-nav__link ><strong>image_buffer_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-pusher-status-get" class=md-nav__link ><strong>image_pusher_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#initialize-post" class=md-nav__link ><strong>initialize_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#pedestal-post" class=md-nav__link ><strong>pedestal_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-pedestal-tiff-get" class=md-nav__link ><strong>preview_pedestal_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-bin-get" class=md-nav__link ><strong>preview_plot_bin_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-get" class=md-nav__link ><strong>preview_plot_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#result-scan-get" class=md-nav__link ><strong>result_scan_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#start-post" class=md-nav__link ><strong>start_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-calibration-get" class=md-nav__link ><strong>statistics_calibration_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-data-collection-get" class=md-nav__link ><strong>statistics_data_collection_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-get" class=md-nav__link ><strong>statistics_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#status-get" class=md-nav__link ><strong>status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#trigger-post" class=md-nav__link ><strong>trigger_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#version-get" class=md-nav__link ><strong>version_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-till-done-post" class=md-nav__link ><strong>wait_till_done_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-until-running-post" class=md-nav__link ><strong>wait_until_running_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-event-code-get" class=md-nav__link ><strong>xfel_event_code_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-pulse-id-get" class=md-nav__link ><strong>xfel_pulse_id_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/AzimIntSettings.html" class=md-nav__link >AzimIntSettings</a> <li class=md-nav__item > <a href="python_client/docs/BraggIntegrationSettings.html" class=md-nav__link >BraggIntegrationSettings</a> <li class=md-nav__item > <a href="python_client/docs/BrokerStatus.html" class=md-nav__link >BrokerStatus</a> <li class=md-nav__item > <a href="python_client/docs/CalibrationStatisticsInner.html" class=md-nav__link >CalibrationStatisticsInner</a> <li class=md-nav__item > <a href="python_client/docs/DarkMaskSettings.html" class=md-nav__link >DarkMaskSettings</a> <li class=md-nav__item > <a href="python_client/docs/DatasetSettings.html" class=md-nav__link >DatasetSettings</a> <li class=md-nav__item > <a href="python_client/docs/DatasetSettingsSmargon.html" class=md-nav__link >DatasetSettingsSmargon</a> <li class=md-nav__item > <a href="python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.html" class=md-nav__link >DatasetSettingsXrayFluorescenceSpectrum</a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html" class=md-nav__link >jfjoch_client.DefaultApi</a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#cancel-post" class=md-nav__link ><strong>cancel_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-azim-int-get" class=md-nav__link ><strong>config_azim_int_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-azim-int-put" class=md-nav__link ><strong>config_azim_int_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-bragg-integration-get" class=md-nav__link ><strong>config_bragg_integration_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-bragg-integration-put" class=md-nav__link ><strong>config_bragg_integration_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-dark-mask-get" class=md-nav__link ><strong>config_dark_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-dark-mask-put" class=md-nav__link ><strong>config_dark_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-detector-get" class=md-nav__link ><strong>config_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-detector-put" class=md-nav__link ><strong>config_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-file-writer-get" class=md-nav__link ><strong>config_file_writer_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-file-writer-put" class=md-nav__link ><strong>config_file_writer_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-conversion-post" class=md-nav__link ><strong>config_image_format_conversion_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-get" class=md-nav__link ><strong>config_image_format_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-put" class=md-nav__link ><strong>config_image_format_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-image-format-raw-post" class=md-nav__link ><strong>config_image_format_raw_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-indexing-get" class=md-nav__link ><strong>config_indexing_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-indexing-put" class=md-nav__link ><strong>config_indexing_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-instrument-get" class=md-nav__link ><strong>config_instrument_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-instrument-put" class=md-nav__link ><strong>config_instrument_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-internal-generator-image-put" class=md-nav__link ><strong>config_internal_generator_image_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-internal-generator-image-tiff-put" class=md-nav__link ><strong>config_internal_generator_image_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-mask-get" class=md-nav__link ><strong>config_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-mask-tiff-get" class=md-nav__link ><strong>config_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-roi-get" class=md-nav__link ><strong>config_roi_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-roi-put" class=md-nav__link ><strong>config_roi_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-get" class=md-nav__link ><strong>config_select_detector_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-select-detector-put" class=md-nav__link ><strong>config_select_detector_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-get" class=md-nav__link ><strong>config_spot_finding_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-spot-finding-put" class=md-nav__link ><strong>config_spot_finding_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-get" class=md-nav__link ><strong>config_user_mask_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-put" class=md-nav__link ><strong>config_user_mask_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-get" class=md-nav__link ><strong>config_user_mask_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-user-mask-tiff-put" class=md-nav__link ><strong>config_user_mask_tiff_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-get" class=md-nav__link ><strong>config_zeromq_metadata_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-metadata-put" class=md-nav__link ><strong>config_zeromq_metadata_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-get" class=md-nav__link ><strong>config_zeromq_preview_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#config-zeromq-preview-put" class=md-nav__link ><strong>config_zeromq_preview_put</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#deactivate-post" class=md-nav__link ><strong>deactivate_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#detector-status-get" class=md-nav__link ><strong>detector_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#fpga-status-get" class=md-nav__link ><strong>fpga_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-clear-post" class=md-nav__link ><strong>image_buffer_clear_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-cbor-get" class=md-nav__link ><strong>image_buffer_image_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-jpeg-get" class=md-nav__link ><strong>image_buffer_image_jpeg_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-image-tiff-get" class=md-nav__link ><strong>image_buffer_image_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-start-cbor-get" class=md-nav__link ><strong>image_buffer_start_cbor_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-buffer-status-get" class=md-nav__link ><strong>image_buffer_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#image-pusher-status-get" class=md-nav__link ><strong>image_pusher_status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#initialize-post" class=md-nav__link ><strong>initialize_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#pedestal-post" class=md-nav__link ><strong>pedestal_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-pedestal-tiff-get" class=md-nav__link ><strong>preview_pedestal_tiff_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-bin-get" class=md-nav__link ><strong>preview_plot_bin_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#preview-plot-get" class=md-nav__link ><strong>preview_plot_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#result-scan-get" class=md-nav__link ><strong>result_scan_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#start-post" class=md-nav__link ><strong>start_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-calibration-get" class=md-nav__link ><strong>statistics_calibration_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-data-collection-get" class=md-nav__link ><strong>statistics_data_collection_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#statistics-get" class=md-nav__link ><strong>statistics_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#status-get" class=md-nav__link ><strong>status_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#trigger-post" class=md-nav__link ><strong>trigger_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#version-get" class=md-nav__link ><strong>version_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-till-done-post" class=md-nav__link ><strong>wait_till_done_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#wait-until-running-post" class=md-nav__link ><strong>wait_until_running_post</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-event-code-get" class=md-nav__link ><strong>xfel_event_code_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/DefaultApi.html#xfel-pulse-id-get" class=md-nav__link ><strong>xfel_pulse_id_get</strong></a> <li class=md-nav__item > <a href="python_client/docs/Detector.html" class=md-nav__link >Detector</a> <li class=md-nav__item > <a href="python_client/docs/DetectorList.html" class=md-nav__link >DetectorList</a> <li class=md-nav__item > <a href="python_client/docs/DetectorListElement.html" class=md-nav__link >DetectorListElement</a> <li class=md-nav__item > <a href="python_client/docs/DetectorModule.html" class=md-nav__link >DetectorModule</a> <li class=md-nav__item > <a href="python_client/docs/DetectorModuleDirection.html" class=md-nav__link >DetectorModuleDirection</a> <li class=md-nav__item > <a href="python_client/docs/DetectorPowerState.html" class=md-nav__link >DetectorPowerState</a> <li class=md-nav__item > <a href="python_client/docs/DetectorSelection.html" class=md-nav__link >DetectorSelection</a> <li class=md-nav__item > <a href="python_client/docs/DetectorSettings.html" class=md-nav__link >DetectorSettings</a> <li class=md-nav__item > <a href="python_client/docs/DetectorState.html" class=md-nav__link >DetectorState</a> <li class=md-nav__item > <a href="python_client/docs/DetectorStatus.html" class=md-nav__link >DetectorStatus</a> <li class=md-nav__item > <a href="python_client/docs/DetectorTiming.html" class=md-nav__link >DetectorTiming</a> <li class=md-nav__item > <a href="python_client/docs/DetectorType.html" class=md-nav__link >DetectorType</a> <li class=md-nav__item > <a href="python_client/docs/ErrorMessage.html" class=md-nav__link >ErrorMessage</a> <li class=md-nav__item > <a href="python_client/docs/FileWriterFormat.html" class=md-nav__link >FileWriterFormat</a> <li class=md-nav__item > <a href="python_client/docs/FileWriterSettings.html" class=md-nav__link >FileWriterSettings</a> <li class=md-nav__item > <a href="python_client/docs/FpgaStatusInner.html" class=md-nav__link >FpgaStatusInner</a> <li class=md-nav__item > <a href="python_client/docs/GeomRefinementAlgorithm.html" class=md-nav__link >GeomRefinementAlgorithm</a> <li class=md-nav__item > <a href="python_client/docs/GridScan.html" class=md-nav__link >GridScan</a> <li class=md-nav__item > <a href="python_client/docs/ImageBufferStatus.html" class=md-nav__link >ImageBufferStatus</a> <li class=md-nav__item > <a href="python_client/docs/ImageFormatSettings.html" class=md-nav__link >ImageFormatSettings</a> <li class=md-nav__item > <a href="python_client/docs/ImagePusherStatus.html" class=md-nav__link >ImagePusherStatus</a> <li class=md-nav__item > <a href="python_client/docs/ImagePusherType.html" class=md-nav__link >ImagePusherType</a> <li class=md-nav__item > <a href="python_client/docs/IndexingAlgorithm.html" class=md-nav__link >IndexingAlgorithm</a> <li class=md-nav__item > <a href="python_client/docs/IndexingSettings.html" class=md-nav__link >IndexingSettings</a> <li class=md-nav__item > <a href="python_client/docs/InstrumentMetadata.html" class=md-nav__link >InstrumentMetadata</a> <li class=md-nav__item > <a href="python_client/docs/IntegrationModel.html" class=md-nav__link >IntegrationModel</a> <li class=md-nav__item > <a href="python_client/docs/JfjochSettings.html" class=md-nav__link >JfjochSettings</a> <li class=md-nav__item > <a href="python_client/docs/JfjochStatistics.html" class=md-nav__link >JfjochStatistics</a> <li class=md-nav__item > <a href="python_client/docs/MeasurementStatistics.html" class=md-nav__link >MeasurementStatistics</a> <li class=md-nav__item > <a href="python_client/docs/PcieDevicesInner.html" class=md-nav__link >PcieDevicesInner</a> <li class=md-nav__item > <a href="python_client/docs/PixelMaskStatistics.html" class=md-nav__link >PixelMaskStatistics</a> <li class=md-nav__item > <a href="python_client/docs/Plot.html" class=md-nav__link >Plot</a> <li class=md-nav__item > <a href="python_client/docs/PlotUnitX.html" class=md-nav__link >PlotUnitX</a> <li class=md-nav__item > <a href="python_client/docs/Plots.html" class=md-nav__link >Plots</a> <li class=md-nav__item > <a href="python_client/docs/RoiAzimList.html" class=md-nav__link >RoiAzimList</a> <li class=md-nav__item > <a href="python_client/docs/RoiAzimuthal.html" class=md-nav__link >RoiAzimuthal</a> <li class=md-nav__item > <a href="python_client/docs/RoiBox.html" class=md-nav__link >RoiBox</a> <li class=md-nav__item > <a href="python_client/docs/RoiBoxList.html" class=md-nav__link >RoiBoxList</a> <li class=md-nav__item > <a href="python_client/docs/RoiCircle.html" class=md-nav__link >RoiCircle</a> <li class=md-nav__item > <a href="python_client/docs/RoiCircleList.html" class=md-nav__link >RoiCircleList</a> <li class=md-nav__item > <a href="python_client/docs/RoiDefinitions.html" class=md-nav__link >RoiDefinitions</a> <li class=md-nav__item > <a href="python_client/docs/RotationAxis.html" class=md-nav__link >RotationAxis</a> <li class=md-nav__item > <a href="python_client/docs/ScanResult.html" class=md-nav__link >ScanResult</a> <li class=md-nav__item > <a href="python_client/docs/ScanResultImagesInner.html" class=md-nav__link >ScanResultImagesInner</a> <li class=md-nav__item > <a href="python_client/docs/SpotFindingSettings.html" class=md-nav__link >SpotFindingSettings</a> <li class=md-nav__item > <a href="python_client/docs/StandardDetectorGeometry.html" class=md-nav__link >StandardDetectorGeometry</a> <li class=md-nav__item > <a href="python_client/docs/TcpSettings.html" class=md-nav__link >TcpSettings</a> <li class=md-nav__item > <a href="python_client/docs/UnitCell.html" class=md-nav__link >UnitCell</a> <li class=md-nav__item > <a href="python_client/docs/ZeromqMetadataSettings.html" class=md-nav__link >ZeromqMetadataSettings</a> <li class=md-nav__item > <a href="python_client/docs/ZeromqPreviewSettings.html" class=md-nav__link >ZeromqPreviewSettings</a> <li class=md-nav__item > <a href="python_client/docs/ZeromqSettings.html" class=md-nav__link >ZeromqSettings</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=rugnux > <h1 id=rugnux--page-root >rugnux<a class=headerlink href="#rugnux--page-root" title="Link to this heading"></a></h1> <p><code class="docutils literal notranslate"><span class=pre >rugnux</span></code> is the <strong>offline</strong> crystallographic data-analysis tool of Jungfraujoch — the data-processing half of the system (see <a class="reference internal" href=NAMING.html ><span class="std std-doc">Naming</span></a> for where the name comes from). It takes an existing HDF5 dataset, runs the full analysis pipeline — spot finding, indexing, geometry refinement, Bragg integration and (optionally) scaling and merging — and writes the results to a <code class="docutils literal notranslate"><span class=pre >_process.h5</span></code> file, plus reflection files (<code class="docutils literal notranslate"><span class=pre >.mtz</span></code>/<code class="docutils literal notranslate"><span class=pre >.cif</span></code>/<code class="docutils literal notranslate"><span class=pre >.hkl</span></code>) when merging is requested.</p> <p>It runs the <em>same</em> analysis code as the online and interactive tools, just driven from the command line over a file rather than a live detector stream.</p> <blockquote> <div><p><strong>Note.</strong> <code class="docutils literal notranslate"><span class=pre >rugnux</span></code> is under very active development. This page describes the tool and its options at a high level; the authoritative, always-current list of options is the program’s own usage message — run <code class="docutils literal notranslate"><span class=pre >rugnux</span></code> with no arguments.</p> </div></blockquote> <section id=where-it-fits-among-the-three-analysis-tools > <h2 id=where-it-fits-among-the-three-analysis-tools >Where it fits among the three analysis tools<a class=headerlink href="#where-it-fits-among-the-three-analysis-tools" title="Link to this heading"></a></h2> <table> <thead> <tr class=row-odd ><th class=head ><p>Tool</p> <th class=head ><p>Mode</p> <th class=head ><p>Driven by</p> <th class=head ><p>Output</p> <tr class=row-even ><td><p><a class="reference internal" href=JFJOCH_BROKER.html ><span class="std std-doc"><code class="docutils literal notranslate"><span class=pre >jfjoch_broker</span></code></span></a></p> <td><p>Online, real-time streaming analysis on FPGA + GPU</p> <td><p>HTTP/REST + ZeroMQ</p> <td><p>Live results and statistics, images streamed to <a class="reference internal" href=JFJOCH_WRITER.html ><span class="std std-doc"><code class="docutils literal notranslate"><span class=pre >jfjoch_writer</span></code></span></a></p> <tr class=row-odd ><td><p><a class="reference internal" href=JFJOCH_VIEWER.html ><span class="std std-doc"><code class="docutils literal notranslate"><span class=pre >jfjoch_viewer</span></code></span></a></p> <td><p>Interactive, on-screen exploration</p> <td><p>Qt desktop application</p> <td><p>On screen; a processing job can write the same files as <code class="docutils literal notranslate"><span class=pre >rugnux</span></code></p> <tr class=row-even ><td><p><strong><code class="docutils literal notranslate"><span class=pre >rugnux</span></code></strong></p> <td><p><strong>Offline batch processing of a stored dataset</strong></p> <td><p><strong>Command-line interface</strong></p> <td><p><strong><code class="docutils literal notranslate"><span class=pre >_process.h5</span></code>, and <code class="docutils literal notranslate"><span class=pre >.mtz</span></code>/<code class="docutils literal notranslate"><span class=pre >.cif</span></code>/<code class="docutils literal notranslate"><span class=pre >.hkl</span></code> when merging</strong></p> </table> <p>Use <code class="docutils literal notranslate"><span class=pre >rugnux</span></code> to re-analyse data after acquisition, to experiment with processing parameters, or to produce merged intensities for downstream structure solution.</p> </section> <section id=hardware > <h2 id=hardware >Hardware<a class=headerlink href="#hardware" title="Link to this heading"></a></h2> <p>As with the rest of Jungfraujoch, <strong>serious performance requires an NVIDIA GPU</strong>. The CUDA build provides the GPU fast-feedback indexer (<code class="docutils literal notranslate"><span class=pre >ffbidx</span></code>) and the GPU FFT indexer (<code class="docutils literal notranslate"><span class=pre >fft</span></code>); without CUDA only the CPU <code class="docutils literal notranslate"><span class=pre >fftw</span></code> indexer is available. Spot finding, integration and scaling run on the CPU and scale with the thread count (<code class="docutils literal notranslate"><span class=pre >-N</span></code>).</p> </section> <section id=input-and-output > <h2 id=input-and-output >Input and output<a class=headerlink href="#input-and-output" title="Link to this heading"></a></h2> <p><strong>Input</strong> is a single Jungfraujoch HDF5 master file (NXmx-based). Spots are always found by <code class="docutils literal notranslate"><span class=pre >rugnux</span></code> itself, including for the two-pass rotation first pass — the spot lists a dataset may already carry were found online, at the acquisition’s threshold and with its ice-band spots already discarded, so reusing them would hide the spot-finding settings from the lattice search.</p> <p><strong>Output</strong> (controlled by <code class="docutils literal notranslate"><span class=pre >-o,</span> <span class=pre >--output-prefix</span></code>, default <code class="docutils literal notranslate"><span class=pre >output</span></code>):</p> <ul> <li><p><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_process.h5</span></code> — NXmx-compliant HDF5 with derived metadata (spots, indexing, integration, azimuthal integration, per-image statistics). See <a class="reference internal" href=HDF5.html ><span class="std std-doc">HDF5 / NeXus data format</span></a> for the layout. Written by default only when <strong>not</strong> merging (i.e. under <code class="docutils literal notranslate"><span class=pre >--no-merge</span></code>); add <code class="docutils literal notranslate"><span class=pre >--write-process-h5</span></code> to also write it when merging.</p> <li><p>Merging is <strong>on by default</strong> (<code class="docutils literal notranslate"><span class=pre >--no-merge</span></code> disables it). The merged reflections are written in <strong>three</strong> formats — each has its uses downstream:</p> <ul class=simple > <li><p><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.mtz</span></code> — CCP4 MTZ (<code class="docutils literal notranslate"><span class=pre >IMEAN</span></code>/<code class="docutils literal notranslate"><span class=pre >I(+)</span></code>/<code class="docutils literal notranslate"><span class=pre >I(-)</span></code>, French–Wilson <code class="docutils literal notranslate"><span class=pre >F</span></code>, <code class="docutils literal notranslate"><span class=pre >FreeR_flag</span></code>) for the CCP4 / phenix reflection tools.</p> <li><p><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.cif</span></code> — mmCIF, for deposition and as the self-describing native format (also carries the merging statistics, ISa, twinning and radiation-damage indicators).</p> <li><p><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.hkl</span></code> — SHELX <strong>HKLF 4</strong> text (<code class="docutils literal notranslate"><span class=pre >h</span> <span class=pre >k</span> <span class=pre >l</span> <span class=pre >I</span> <span class=pre >σ(I)</span></code>, fixed <code class="docutils literal notranslate"><span class=pre >3I4,2F8.2</span></code>), the direct input for <strong>SHELXC / ANODE / SHELXD</strong>. Bijvoet mates are written separately (<code class="docutils literal notranslate"><span class=pre >I(+)</span></code> at <code class="docutils literal notranslate"><span class=pre >+hkl</span></code>, <code class="docutils literal notranslate"><span class=pre >I(-)</span></code> at <code class="docutils literal notranslate"><span class=pre >-hkl</span></code>) so the anomalous signal is preserved; intensities are put on a common scale so the largest value fits the fixed-width field (the absolute scale is irrelevant to SHELXC/ANODE), and the file ends with the <code class="docutils literal notranslate"><span class=pre >0</span> <span class=pre >0</span> <span class=pre >0</span></code> terminator record.</p> </ul> <p>All three carry the <strong>refined unit cell</strong> (from rotation indexing) and the <strong>space group determined from systematic absences</strong> (constrained to the indexed lattice symmetry). No-reference scaling additionally emits per-iteration <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_iterN_scale.dat</span></code>.</p> <li><p><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_report.txt</span></code> — the <strong>results report</strong>: what the run determined, in a form both a person and a beamline script can read. Always written, next to the files above. See <a class="reference internal" href="#the-results-report">The results report</a> below.</p> </ul> <p>Merged statistics (⟨I/σ⟩, CC1/2, completeness, …), the error model and timing are printed to the console. By default the written resolution is trimmed automatically where CC1/2 falls off (<code class="docutils literal notranslate"><span class=pre >--resolution-cutoff</span> <span class=pre >cc-logistic</span></code>, CC1/2 target 0.30); set <code class="docutils literal notranslate"><span class=pre >--scaling-high-resolution</span></code> to fix the limit by hand, or <code class="docutils literal notranslate"><span class=pre >--resolution-cutoff</span> <span class=pre >off</span></code> to keep the full range.</p> <section id=reflection-file-conventions > <h3 id=reflection-file-conventions >Reflection-file conventions<a class=headerlink href="#reflection-file-conventions" title="Link to this heading"></a></h3> <p><strong>mmCIF.</strong> Standard items carry their standard meanings — <code class="docutils literal notranslate"><span class=pre >_refln.intensity_meas</span></code> / <code class="docutils literal notranslate"><span class=pre >_intensity_sigma</span></code>, the <code class="docutils literal notranslate"><span class=pre >pdbx_I_plus</span></code>/<code class="docutils literal notranslate"><span class=pre >pdbx_I_minus</span></code> and <code class="docutils literal notranslate"><span class=pre >pdbx_F_plus</span></code>/<code class="docutils literal notranslate"><span class=pre >pdbx_F_minus</span></code> anomalous pairs, <code class="docutils literal notranslate"><span class=pre >_reflns.*</span></code> and <code class="docutils literal notranslate"><span class=pre >_reflns_shell.*</span></code> for the merging statistics, <code class="docutils literal notranslate"><span class=pre >_reflns.B_iso_Wilson_estimate</span></code> for the Wilson B, and <code class="docutils literal notranslate"><span class=pre >_cell.*</span></code> / <code class="docutils literal notranslate"><span class=pre >_diffrn_radiation_wavelength.wavelength</span></code> for the geometry.</p> <p>Anything rugnux reports that has no standard item is written under a <strong><code class="docutils literal notranslate"><span class=pre >jfjoch_</span></code></strong> prefix, inside the standard category it belongs to. That is a deliberate choice: a reader that does not know these items ignores them, and one that does can find them without guessing.</p> <table> <thead> <tr class=row-odd ><th class=head ><p>item</p> <th class=head ><p>meaning</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_diffrn_ISa</span></code></p> <td><p>Asymptotic I/σ in <strong>XDS’s sense</strong>: the whole-range <code class="docutils literal notranslate"><span class=pre >1/√(a·b)</span></code> of the error model, so it can be read directly against a <code class="docutils literal notranslate"><span class=pre >CORRECT.LP</span></code></p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_diffrn_ISa_asymptotic</span></code></p> <td><p>The <strong>strong-reflection</strong> tier — the counting-subtracted scatter of well-measured groups. XDS has no equivalent, and it can only ever be the more optimistic of the two. Rotation path only</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_error_model_a</span></code>, <code class="docutils literal notranslate"><span class=pre >_b</span></code></p> <td><p>The error model in XDS’s convention, <code class="docutils literal notranslate"><span class=pre >σ²</span> <span class=pre >=</span> <span class=pre >a(σ₀²</span> <span class=pre >+</span> <span class=pre >b·I²)</span></code>, so the ISa above is re-derivable from the file rather than taken on trust</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_second_moment_I</span></code></p> <td><p>Twinning second moment ⟨I²⟩/⟨I⟩² — 2.00 untwinned, 1.50 for a perfect twin</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_L_test_mean_abs_L</span></code>, <code class="docutils literal notranslate"><span class=pre >_L_test_mean_L_squared</span></code></p> <td><p>Padilla–Yeates L-test. ⟨|L|⟩ is 0.500 untwinned / 0.375 for a perfect twin; ⟨L²⟩ is 0.333 / 0.200. Written only when the test found pairs</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_radiation_damage_relative_B</span></code></p> <td><p>Relative <em>B</em> from the first to the last rotation batch (Ų); positive is the usual direction, high-resolution intensity fading with dose</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >_jfjoch_radiation_damage_batch.*</span></code></p> <td><p>Per-batch loop: <code class="docutils literal notranslate"><span class=pre >id</span></code>, <code class="docutils literal notranslate"><span class=pre >rotation_start_deg</span></code>, <code class="docutils literal notranslate"><span class=pre >relative_B</span></code></p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >_diffrn_detector.jfjoch_distance_mm</span></code>, <code class="docutils literal notranslate"><span class=pre >_jfjoch_beam_center_x_pxl</span></code>, <code class="docutils literal notranslate"><span class=pre >_jfjoch_beam_center_y_pxl</span></code></p> <td><p>The refined detector geometry actually used, which is not otherwise recoverable from the reflection file</p> </table> <blockquote> <div><p><strong>Compatibility note.</strong> Before rc.161, <code class="docutils literal notranslate"><span class=pre >_reflns.jfjoch_diffrn_ISa</span></code> carried the <em>asymptote</em>, not the whole-range value. There is no version marker inside the file, so a number taken from an older <code class="docutils literal notranslate"><span class=pre >.cif</span></code> is not comparable with one taken from a newer one.</p> </div></blockquote> <p><strong>SHELX HKLF 4</strong> (<code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.hkl</span></code>). Fixed-format <code class="docutils literal notranslate"><span class=pre >3I4,2F8.2</span></code> — <code class="docutils literal notranslate"><span class=pre >h</span> <span class=pre >k</span> <span class=pre >l</span> <span class=pre >I</span> <span class=pre >σ(I)</span></code>, one record per reflection, terminated by a <code class="docutils literal notranslate"><span class=pre >0</span> <span class=pre >0</span> <span class=pre >0</span></code> record — which is what <strong>SHELXC</strong>, <strong>SHELXD</strong> and <strong>ANODE</strong> expect. Two properties worth knowing before using it:</p> <ul class=simple > <li><p><strong>Bijvoet mates are written separately</strong>, <code class="docutils literal notranslate"><span class=pre >I(+)</span></code> at <code class="docutils literal notranslate"><span class=pre >+hkl</span></code> and <code class="docutils literal notranslate"><span class=pre >I(-)</span></code> at <code class="docutils literal notranslate"><span class=pre >-hkl</span></code>, so the anomalous differences survive into SHELXC; a reflection with no anomalous split is written once, as its mean.</p> <li><p><strong>Intensities are rescaled</strong> by a single global factor so the largest value fits the <code class="docutils literal notranslate"><span class=pre >F8.2</span></code> field. <code class="docutils literal notranslate"><span class=pre >I</span></code> and <code class="docutils literal notranslate"><span class=pre >σ(I)</span></code> share that factor, so every ratio — and therefore the anomalous signal — is untouched, but the absolute scale is not meaningful. This matters only if you intend to compare magnitudes with another file; SHELXC and ANODE use ratios alone.</p> </ul> </section> </section> <section id=the-results-report > <h2 id=the-results-report >The results report<a class=headerlink href="#the-results-report" title="Link to this heading"></a></h2> <p><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_report.txt</span></code> records <strong>what the run determined</strong>, next to the reflection files. It is written on every <code class="docutils literal notranslate"><span class=pre >--mode</span> <span class=pre >mx</span></code> and <code class="docutils literal notranslate"><span class=pre >--mode</span> <span class=pre >scale</span></code> run that has an output prefix — there is no option to enable or disable it. Two cases follow from that:</p> <ul class=simple > <li><p>An <strong>empty output prefix</strong> (<code class="docutils literal notranslate"><span class=pre >-o</span> <span class=pre >""</span></code>, the “compute the statistics, persist nothing” mode) writes nothing, the report included.</p> <li><p><strong><code class="docutils literal notranslate"><span class=pre >--no-merge</span></code></strong> still writes a report. It determined an indexing and a geometry result, and those are recorded; the merging section then says <code class="docutils literal notranslate"><span class=pre >MERGE=</span> <span class=pre >NOT_PERFORMED</span></code> rather than being omitted, so the absence is a statement and not something a reader has to infer.</p> </ul> <p>The report is never allowed to fail a run: if it cannot be written (unwritable path, full disk) the failure is logged as a warning and the run finishes normally.</p> <section id=format > <h3 id=format >Format<a class=headerlink href="#format" title="Link to this heading"></a></h3> <p>The model is XDS’s <code class="docutils literal notranslate"><span class=pre >CORRECT.LP</span></code>: prose and tables a crystallographer reads top to bottom, with a structure a script can consume without parsing prose.</p> <ul class=simple > <li><p><strong><code class="docutils literal notranslate"><span class=pre >KEY=</span> <span class=pre >value</span></code> assignment lines.</strong> Every number worth extracting is one, so a consumer gets it with a single <code class="docutils literal notranslate"><span class=pre >grep</span> <span class=pre >'^ISA=</span> <span class=pre >'</span></code> and never has to read a sentence. Key names are stable.</p> <li><p><strong>Fixed-width tables</strong> with a stable header row for anything that is genuinely tabular — the resolution shells, the space-group candidates, the sweep-quality ranges.</p> <li><p><strong><code class="docutils literal notranslate"><span class=pre >WARNING:</span></code> lines</strong>, one per finding, in plain English: <code class="docutils literal notranslate"><span class=pre >WARNING:</span> <span class=pre >Frames</span> <span class=pre >500-600</span> <span class=pre >out</span> <span class=pre >of</span> <span class=pre >beam</span> <span class=pre >(10.1</span> <span class=pre >deg,</span> <span class=pre >scale</span> <span class=pre >0.12</span> <span class=pre >and</span> <span class=pre >CC</span> <span class=pre >0.30</span> <span class=pre >of</span> <span class=pre >the</span> <span class=pre >run,</span> <span class=pre >2%</span> <span class=pre >scaled)</span></code>. <code class="docutils literal notranslate"><span class=pre >grep</span> <span class=pre >'^WARNING:'</span></code> finds every one.</p> <li><p><strong>Section banners</strong> (<code class="docutils literal notranslate"><span class=pre >***…***</span></code> around a numbered title) delimiting the blocks.</p> </ul> <p><code class="docutils literal notranslate"><span class=pre >REPORT_VERSION=</span></code> is the format’s own version. Key names, table columns and the reason vocabulary below are an interface other software may depend on: they do not change without that number moving.</p> <p>Sections, in order: <code class="docutils literal notranslate"><span class=pre >1.</span> <span class=pre >DATA</span> <span class=pre >SET</span></code>, <code class="docutils literal notranslate"><span class=pre >2.</span> <span class=pre >INDEXING</span></code>, <code class="docutils literal notranslate"><span class=pre >3.</span> <span class=pre >GEOMETRY</span> <span class=pre >POST-REFINEMENT</span></code> (rotation only), <code class="docutils literal notranslate"><span class=pre >4.</span> <span class=pre >SPACE</span> <span class=pre >GROUP</span> <span class=pre >DETERMINATION</span></code>, <code class="docutils literal notranslate"><span class=pre >5.</span> <span class=pre >SCALING</span> <span class=pre >AND</span> <span class=pre >MERGING</span></code>, <code class="docutils literal notranslate"><span class=pre >6.</span> <span class=pre >TWINNING</span></code>, <code class="docutils literal notranslate"><span class=pre >7.</span> <span class=pre >RADIATION</span> <span class=pre >DAMAGE</span></code>, <code class="docutils literal notranslate"><span class=pre >8.</span> <span class=pre >SWEEP</span> <span class=pre >QUALITY</span></code>, <code class="docutils literal notranslate"><span class=pre >9.</span> <span class=pre >WARNINGS</span></code>.</p> <p><strong>Which pass.</strong> A rotation run integrates twice — once at the geometry in the input file (<code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_01.*</span></code>), then again at the post-refined geometry (<code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.*</span></code>) — and can integrate a third time if a guard rejects the second pass. There is <strong>one</strong> report, for the pass that became the canonical output, and <code class="docutils literal notranslate"><span class=pre >PASS=</span></code> / <code class="docutils literal notranslate"><span class=pre >PASS_DECISION=</span></code> in section 1 say which pass that is and on what evidence, so no number in the file is ambiguous about which geometry produced it.</p> <p><strong>Not in the report:</strong> timing, frame rates, thread counts, per-image progress and library banners. Those are process, not result, and stay on stdout.</p> </section> <section id=sweep-quality-and-the-reason-vocabulary > <h3 id=sweep-quality-and-the-reason-vocabulary >Sweep quality and the reason vocabulary<a class=headerlink href="#sweep-quality-and-the-reason-vocabulary" title="Link to this heading"></a></h3> <p>Section 8 lists the stretches of the sweep over which the crystal delivered much less than the rest of the run — the feedback a beamline control system needs to tell an operator that a crystal should be recentred or recollected. Nothing is excluded on the strength of it; the frames still carry signal, and this is a message for the beamline, not a filter.</p> <div class="highlight-default notranslate"><div class=highlight ><pre><span></span><span class=n >SWEEP_QUALITY_STATUS</span><span class=o >=</span> <span class=n >COMPUTED</span>
<span class=n >SWEEP_QUALITY_COUNT</span><span class=o >=</span> <span class=mi >1</span>
<span class=n >SWEEP_QUALITY_REASONS</span><span class=o >=</span> <span class=n >no_diffraction</span> <span class=n >crystal_out_of_beam</span> <span class=n >weak_diffraction</span> <span class=n >loss_of_centring</span> <span class=n >radiation_damage</span>
<span class=n >SWEEP_ROTATION</span><span class=o >=</span> <span class=mf >360.0</span>
<span class=n >FLUX_PEAK_TO_TROUGH</span><span class=o >=</span> <span class=mf >1.03</span>
<span class=n >SCALE_MODULATION_PEAK_TO_TROUGH</span><span class=o >=</span> <span class=mf >1.00</span>
<span class=n >FIRST_IMAGE</span> <span class=n >LAST_IMAGE</span> <span class=n >N_IMAGES</span> <span class=n >ROTATION</span> <span class=n >REASON</span> <span class=n >SEVERITY</span> <span class=n >SCALE</span> <span class=n >CC</span> <span class=n >INDEXED</span>
<span class=o >-----------</span> <span class=o >-----------</span> <span class=o >---------</span> <span class=o >--------</span> <span class=o >--------------------</span> <span class=o >--------</span> <span class=o >------</span> <span class=o >------</span> <span class=o >--------</span>
<span class=mi >500</span> <span class=mi >600</span> <span class=mi >101</span> <span class=mf >10.1</span> <span class=n >crystal_out_of_beam</span> <span class=mf >0.83</span> <span class=mf >0.12</span> <span class=mf >0.30</span> <span class=mf >0.02</span>
<span class=o >-----------</span> <span class=o >-----------</span> <span class=o >---------</span> <span class=o >--------</span> <span class=o >--------------------</span> <span class=o >--------</span> <span class=o >------</span> <span class=o >------</span> <span class=o >--------</span>
</pre></div> </div> <p><code class="docutils literal notranslate"><span class=pre >SWEEP_QUALITY_STATUS</span></code> distinguishes <strong><code class="docutils literal notranslate"><span class=pre >COMPUTED</span></code></strong> (the diagnostic ran; a count of 0 means the sweep was clean throughout) from <strong><code class="docutils literal notranslate"><span class=pre >NOT_COMPUTED</span></code></strong> (it did not run — no scaling and merging, or stills data). A consumer must not read a missing table or a zero count as “clean” without checking it. <code class="docutils literal notranslate"><span class=pre >SWEEP_QUALITY_REASONS</span></code> lists the whole vocabulary this version can emit, so an unknown code is distinguishable from a missing one.</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Reason code</p> <th class=head ><p>Meaning</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >no_diffraction</span></code></p> <td><p>The range recorded essentially no diffraction from the indexed lattice.</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >crystal_out_of_beam</span></code></p> <td><p>Frames were lost: over the range a per-image scale could be fitted far less often than over the run.</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >weak_diffraction</span></code></p> <td><p>The frames all still index, but with much less intensity — the cause was not determined.</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >loss_of_centring</span></code></p> <td><p>One cycle of modulation per revolution: the crystal is off the rotation axis.</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >radiation_damage</span></code></p> <td><p>The range runs to the end of a sweep whose quality was already decaying.</p> </table> <p>The vocabulary is <strong>closed and stable</strong>: a code is never renamed, and never reused for a different meaning. New codes are only ever added, and adding one moves <code class="docutils literal notranslate"><span class=pre >REPORT_VERSION</span></code>.</p> <p>The columns are: <code class="docutils literal notranslate"><span class=pre >FIRST_IMAGE</span></code>/<code class="docutils literal notranslate"><span class=pre >LAST_IMAGE</span></code> — inclusive, in processed-image ordinals (the numbering of <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_image.dat</span></code> and of every other per-image array <code class="docutils literal notranslate"><span class=pre >rugnux</span></code> writes; with <code class="docutils literal notranslate"><span class=pre >-s</span></code>/<code class="docutils literal notranslate"><span class=pre >--stride</span></code> the source image is <code class="docutils literal notranslate"><span class=pre >start</span> <span class=pre >+</span> <span class=pre >ordinal</span> <span class=pre >*</span> <span class=pre >stride</span></code>); <code class="docutils literal notranslate"><span class=pre >ROTATION</span></code> — the width of the range in degrees; <code class="docutils literal notranslate"><span class=pre >SEVERITY</span></code> — the fraction of the run’s typical diffracting power missing over the range, 0 (as good as the run) to 1 (nothing at all); <code class="docutils literal notranslate"><span class=pre >SCALE</span></code> and <code class="docutils literal notranslate"><span class=pre >CC</span></code> — the range’s mean per-image scale and CC-to-merge relative to the run median; <code class="docutils literal notranslate"><span class=pre >INDEXED</span></code> — the fraction of the range’s frames that were scaled at all. Every range also appears as a <code class="docutils literal notranslate"><span class=pre >WARNING:</span></code> sentence in section 9.</p> <p>The same finding is written <strong>per image</strong> into the <code class="docutils literal notranslate"><span class=pre >_process.h5</span></code> as <code class="docutils literal notranslate"><span class=pre >/entry/MX/sweepQuality</span></code>, when one is written — see <a class="reference internal" href="HDF5.html#entry-mx-spot-finding-and-indexing-cxi-style"><span class="std std-ref">HDF5</span></a>.</p> </section> </section> <section id=validating-against-a-model-rugnux-model > <h2 id=validating-against-a-model-rugnux-model >Validating against a model (<code class="docutils literal notranslate"><span class=pre >rugnux</span> <span class=pre >--model</span></code>)<a class=headerlink href="#validating-against-a-model-rugnux-model" title="Link to this heading"></a></h2> <p>Given a PDB atomic model of the same structure, <code class="docutils literal notranslate"><span class=pre >--model</span> <span class=pre >model.pdb</span></code> scales the model structure factors to the merged amplitudes — fitting a flat bulk-solvent contribution and an overall anisotropic <em>B</em> — and reports <strong>R-work / R-free</strong> and the mean 2Fo-Fc density at the atom centres. It also writes <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_2fofc.ccp4</span></code>, <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_fofc.ccp4</span></code> and <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_maps.mtz</span></code> next to the merged reflections. Nothing about the model is refined; it is only re-fractionalized into the data cell, so a deposited model with a slightly different cell still lines up.</p> <p>It is a <em>data-quality lens</em>, independent of the internal statistics: R-free measures the merged intensities against external truth, where CC1/2 and R<sub>meas</sub> only measure them against themselves. It also settles the two things merged intensities alone cannot: the enantiomorph (data merged in P4<sub>1</sub>2<sub>1</sub>2 against a P4<sub>3</sub>2<sub>1</sub>2 model are reindexed into the model’s hand), and — when no reference MTZ has already fixed it — a merohedral indexing ambiguity, by keeping the candidate reindexing with the lowest R-free.</p> </section> <section id=re-scaling-and-re-merging-rugnux-mode-scale > <h2 id=re-scaling-and-re-merging-rugnux-mode-scale >Re-scaling and re-merging (<code class="docutils literal notranslate"><span class=pre >rugnux</span> <span class=pre >--mode</span> <span class=pre >scale</span></code>)<a class=headerlink href="#re-scaling-and-re-merging-rugnux-mode-scale" title="Link to this heading"></a></h2> <p>The <code class="docutils literal notranslate"><span class=pre >scale</span></code> mode re-scales and merges the <em>already-integrated</em> reflections stored in a <code class="docutils literal notranslate"><span class=pre >_process.h5</span></code> file, without re-running spot finding or integration. Use it to re-merge quickly with a different space group, resolution limit, anomalous setting or reference MTZ. It reuses the same <code class="docutils literal notranslate"><span class=pre >-o/-N/-s/-e/-S/-A/-B/-z/--scaling-*</span></code> options as the full run, and (unlike the full pipeline) does not run a space-group search, so pass <code class="docutils literal notranslate"><span class=pre >-S</span></code> for the correct symmetry.</p> </section> <section id=detector-calibration-from-powder-rings-rugnux-mode-calibration > <h2 id=detector-calibration-from-powder-rings-rugnux-mode-calibration >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 class=headerlink href="#detector-calibration-from-powder-rings-rugnux-mode-calibration" title="Link to this heading"></a></h2> <p>The <code class="docutils literal notranslate"><span class=pre >calibration</span></code> mode determines the detector geometry — PONI <em>x</em>/<em>y</em>, the two tilts rot1/rot2 and the distance — from the powder rings of a calibrant, and writes it as a pyFAI <strong><code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.poni</span></code></strong> file alongside a printed report of how far each parameter moved from the header. Bragg data pin the beam centre worst (it is gauge-coupled to the crystal orientation); a powder ring has no orientation to be coupled to, so this is the measurement that fixes it.</p> <div class="highlight-default notranslate"><div class=highlight ><pre><span></span><span class=n >rugnux</span> <span class=o >--</span><span class=n >mode</span> <span class=n >calibration</span> <span class=o >--</span><span class=n >calibrant</span> <span class=n >lab6</span> <span class=o >-</span><span class=n >N</span> <span class=mi >8</span> <span class=o >-</span><span class=n >o</span> <span class=n >det</span> <span class=n >LaB6_master</span><span class=o >.</span><span class=n >h5</span>
</pre></div> </div> <p><code class="docutils literal notranslate"><span class=pre >--calibrant</span></code> takes <code class="docutils literal notranslate"><span class=pre >lab6</span></code>, <code class="docutils literal notranslate"><span class=pre >agbh</span></code> (silver behenate), <code class="docutils literal notranslate"><span class=pre >ceo2</span></code>, <code class="docutils literal notranslate"><span class=pre >si</span></code> or <code class="docutils literal notranslate"><span class=pre >ice</span></code>, case-insensitively. <strong><code class="docutils literal notranslate"><span class=pre >ice</span></code></strong> calibrates a real experiment against its own ice rings — no calibrant exposure needed — and is the reason a calibrant is a list of ring positions rather than a unit cell: hexagonal ice is P6<sub>3</sub>/mmc, so rings enumerated from its cell would include systematically absent ones.</p> <p><code class="docutils literal notranslate"><span class=pre >--calibration</span></code> picks how the rings are measured, and <strong>both use the whole dataset</strong> — <code class="docutils literal notranslate"><span class=pre >-s</span></code>/<code class="docutils literal notranslate"><span class=pre >-e</span></code>/<code class="docutils literal notranslate"><span class=pre >-t</span></code> select which images:</p> <ul class=simple > <li><p><strong><code class="docutils literal notranslate"><span class=pre >rings</span></code></strong> (default) sums the (<em>q</em> × azimuth) azimuthal profile over every processed image into one map and fits the ring arcs in it. A powder ring is an arc, not a set of spots, and the summed profile measures it at every azimuth with all the run’s counts behind it. It needs the profile to be binned in azimuth, so this mode defaults <code class="docutils literal notranslate"><span class=pre >--azim-phi-bins</span></code> to 32.</p> <li><p><strong><code class="docutils literal notranslate"><span class=pre >spots</span></code></strong> pools the found spots of every processed image and fits those. It determines the centre from scratch (a Hough circle vote, which quantises it to a whole pixel) and then refines.</p> </ul> <p>Both routes read the ring position out of a binned profile or a spot centroid, so the radial sampling matters: at a long detector distance the default 0.01 Å⁻¹ <em>q</em> bin is several pixels wide and quantises the <code class="docutils literal notranslate"><span class=pre >rings</span></code> route accordingly — pass a finer <code class="docutils literal notranslate"><span class=pre >--azim-q-spacing</span></code> there (the total <em>q</em> × azimuth bin count must stay under 65534).</p> <p>The report prints the fitted geometry, the scatter of the ring points about the fitted rings and the standard error that implies on the centre. That error is <em>formal</em>: it measures the scatter of the points, not whether the rings themselves are trustworthy, so it stays small when a fit goes wrong for a structural reason — one visible ring, or ice that is textured rather than smooth.</p> <p>Both the PONI (the point of normal incidence, which is what a <code class="docutils literal notranslate"><span class=pre >.poni</span></code> file stores) and the direct beam (where the beam lands, which is what most other programs call the beam centre) are printed. They differ by <em>distance</em> × tan(rot) once the detector is tilted, which on a 0.3° tilt at 300 mm is several pixels — enough to look like a disagreement with another program when there is none.</p> </section> <section id=quick-start > <h2 id=quick-start >Quick start<a class=headerlink href="#quick-start" title="Link to this heading"></a></h2> <section id=rotation-data > <h3 id=rotation-data >Rotation data<a class=headerlink href="#rotation-data" title="Link to this heading"></a></h3> <p>Index, integrate, scale and merge a rotation sweep, fully de novo:</p> <div class="highlight-default notranslate"><div class=highlight ><pre><span></span><span class=n >rugnux</span> <span class=n >rotation_master</span><span class=o >.</span><span class=n >h5</span> \
<span class=o >-</span><span class=n >o</span> <span class=n >rotation_run</span> <span class=o >-</span><span class=n >N</span> <span class=mi >32</span> \
<span class=o >--</span><span class=n >scaling</span><span class=o >-</span><span class=n >high</span><span class=o >-</span><span class=n >resolution</span> <span class=mf >1.4</span>
</pre></div> </div> <p>Because the dataset carries a rotation goniometer axis, it is processed as <strong>rotation data by default</strong>: two-pass rotation indexing (index the sweep once, then process every frame against that lattice) with the <strong><code class="docutils literal notranslate"><span class=pre >rot3d</span></code></strong> partiality model (rotation partials combined into 3D fulls). Scaling and merging run <strong>by default</strong> (for both rotation and stills; <code class="docutils literal notranslate"><span class=pre >--no-merge</span></code> turns them off); the unit cell is taken from the rotation indexer and the space group is determined from systematic absences, and both are written into the merged <code class="docutils literal notranslate"><span class=pre >.cif</span></code>.</p> <p>Run <strong>fully de novo</strong> (no <code class="docutils literal notranslate"><span class=pre >-C</span></code>/<code class="docutils literal notranslate"><span class=pre >-S</span></code>) for the best result — supplying a cell or space group up front tends to <em>degrade</em> low-symmetry cases. <code class="docutils literal notranslate"><span class=pre >--scaling-high-resolution</span></code> (set it to your expected resolution) sharpens both the space-group search and the error model. To tune the first pass use <code class="docutils literal notranslate"><span class=pre >--two-pass-rotation=100</span></code> (or <code class="docutils literal notranslate"><span class=pre >-R100</span></code> — the first-pass image count); to force the sweep to be treated as independent stills use <code class="docutils literal notranslate"><span class=pre >--force-still</span></code>.</p> <p>By default a rotation run also <strong>post-refines the geometry</strong> in a second pass: the first pass integrates and merges at the header geometry, then the detector distance + beam centre and the crystal cell / rotation-axis are refined against the merged fulls (cross-validated, and committed only for a small &lt; 1 % move, with the gauge-weak beam centre restrained toward the header), and the second pass re-indexes de novo and re-integrates at the refined geometry. The refined pass is the canonical <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_*</span></code> output; the header-geometry pass is kept alongside as <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_01_*</span></code> for comparison. Disable it with <code class="docutils literal notranslate"><span class=pre >--rotation-no-postrefine</span></code>.</p> <p>After the per-frame scale-fulls step, rotation scaling applies three <strong>correction surfaces</strong>, <strong>on by default</strong> (<code class="docutils literal notranslate"><span class=pre >--no-scaling-corrections</span></code> disables all):</p> <ul class=simple > <li><p><strong>Decay</strong> — a global Debye–Waller relative-<em>B</em> over the run, for the radiation damage that weakens later frames more at high resolution (a resolution×time systematic the resolution-flat per-frame scale cannot remove). It only engages when the total relative-<em>B</em> exceeds a physical floor (2 Ų). An optional <code class="docutils literal notranslate"><span class=pre >--relative-b[=deg]</span></code> extends this single global rate to a smooth per-batch relative-<em>B</em> curve (default 10°-of-rotation batches when bare, off otherwise), cross-validated like the surfaces here, for crystals whose decay is non-linear in dose.</p> <li><p><strong>Absorption</strong> — a smooth multiplicative factor over the diffracted-beam direction in the goniometer frame (path length through the crystal). Negligible at hard X-rays / thin crystals; it matters at low photon energy. Its benefit shows up most on model-based metrics: a smooth absorption error largely cancels among symmetry mates (little effect on the error model / ISa) but still biases the intensities, so it measurably lowers <em>R</em><sub>free</sub>.</p> <li><p><strong>Modulation</strong> — a smooth multiplicative factor over the position where a reflection lands on the detector (a flat-field: detector-response and geometric systematics that vary across the detector plane). Symmetry-equivalents of one reflection land at different detector positions as the crystal rotates, which over-determines the surface. Because it lives in the detector frame (not the rotation) the same correction concept applies to stills. This is the largest of the three on JUNGFRAU data — it lowers <em>R</em><sub>meas</sub> by several to tens of percent on datasets that carry a detector systematic, while holding or improving CC<sub>1/2</sub> and the anomalous signal.</p> </ul> <p>All three are <strong>cross-validated</strong> — fitted on even-numbered frames and kept only if they improve the held-out odd-frame symmetry-equivalent agreement by a clear margin (and vice versa). The agreement is scored as a σ-independent, <em>R</em><sub>meas</sub>-like fractional deviation, so a surface can never pass cross-validation by merely reshaping the sigmas; where the systematic is absent the surface is a no-op rather than a source of added noise, which is why they are safe to leave on.</p> <p>Independently of any correction, a rotation run prints a <strong>radiation-damage report</strong> — the per-image scale correlation-to-merge and mosaicity versus dose, and the relative <em>B</em>-factor change over the run (first→last) together with a per-batch relative-<em>B</em> curve, also written to the merged mmCIF. It is a data-quality-vs-dose diagnostic and never alters the merged intensities. A batch whose data cannot support a measurement prints <code class="docutils literal notranslate"><span class=pre >-</span></code> instead of a value, and the first→last number is printed only where a straight line describes the curve — damage is progressive, so a curve that dips and recovers is a disturbance of the sweep, not dose, and the report says so and points at the sweep-quality section (<code class="docutils literal notranslate"><span class=pre >RADIATION_DAMAGE_RELATIVE_B=</span> <span class=pre >NOT_A_TREND</span></code>).</p> </section> <section id=still-serial-data > <h3 id=still-serial-data >Still / serial data<a class=headerlink href="#still-serial-data" title="Link to this heading"></a></h3> <p>A dataset with <strong>no goniometer axis</strong> (e.g. a serial grid scan) is processed as <strong>independent stills automatically</strong> — no flag needed. Known-cell indexing with the GPU fast-feedback indexer, then merge against a reference structure:</p> <div class="highlight-default notranslate"><div class=highlight ><pre><span></span><span class=n >rugnux</span> <span class=n >serial_master</span><span class=o >.</span><span class=n >h5</span> \
<span class=o >-</span><span class=n >o</span> <span class=n >serial_run</span> <span class=o >-</span><span class=n >N</span> <span class=mi >32</span> \
<span class=o >-</span><span class=n >X</span> <span class=n >ffbidx</span> <span class=o >-</span><span class=n >C</span> <span class=mi >79</span><span class=p >,</span><span class=mi >79</span><span class=p >,</span><span class=mi >38</span><span class=p >,</span><span class=mi >90</span><span class=p >,</span><span class=mi >90</span><span class=p >,</span><span class=mi >90</span> <span class=o >-</span><span class=n >S</span> <span class=mi >96</span> \
<span class=o >-</span><span class=n >z</span> <span class=n >reference</span><span class=o >.</span><span class=n >mtz</span> \
<span class=o >--</span><span class=n >scaling</span><span class=o >-</span><span class=n >high</span><span class=o >-</span><span class=n >resolution</span> <span class=mf >1.8</span>
</pre></div> </div> <p><code class="docutils literal notranslate"><span class=pre >ffbidx</span></code> requires a known cell (<code class="docutils literal notranslate"><span class=pre >-C</span></code>) and is the indexer of choice for sparse serial stills. The self-calibrating spot finder is on by default for both workflows (<code class="docutils literal notranslate"><span class=pre >--no-adaptive-spots</span></code> turns it off), and for serial stills leave <code class="docutils literal notranslate"><span class=pre >--min-pix-per-spot</span></code> <strong>unset</strong> so it is chosen per image — across the still-target battery this combination raises the indexing rate and typically extends resolution over a fixed threshold and fixed min-pix, at equal or better CC½. (You can still pin a fixed threshold with <code class="docutils literal notranslate"><span class=pre >--spot-sigma</span></code> / <code class="docutils literal notranslate"><span class=pre >--spot-threshold</span></code> and a fixed min-pix with <code class="docutils literal notranslate"><span class=pre >--min-pix-per-spot</span></code>.) If a dataset <em>does</em> carry a goniometer axis but you want per-frame stills processing anyway, add <code class="docutils literal notranslate"><span class=pre >--force-still</span></code>.</p> </section> </section> <section id=command-line-options > <h2 id=command-line-options >Command-line options<a class=headerlink href="#command-line-options" title="Link to this heading"></a></h2> <p>General:</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >-o,</span> <span class=pre >--output-prefix</span> <span class=pre >&lt;txt&gt;</span></code></p> <td><p>Output file prefix (default: <code class="docutils literal notranslate"><span class=pre >output</span></code>)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-N,</span> <span class=pre >--threads</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Number of worker threads (default: all hardware threads)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >-s,</span> <span class=pre >--start-image</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>First image to process (default: 0)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-e,</span> <span class=pre >--end-image</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Last image to process (default: all)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >-t,</span> <span class=pre >--stride</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Process every <em>n</em>-th image (default: 1)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-v,</span> <span class=pre >--verbose</span></code></p> <td><p>Verbose output</p> </table> <p>Mode — <code class="docutils literal notranslate"><span class=pre >--mode</span> <span class=pre >&lt;name&gt;</span></code> (default <code class="docutils literal notranslate"><span class=pre >mx</span></code>):</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Value</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >mx</span></code></p> <td><p>Full analysis — spot finding, indexing, integration and merging</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >azint</span></code></p> <td><p>Only azimuthal integration (no spot finding/indexing); writes <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;_process.h5</span></code></p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >scale</span></code></p> <td><p>Only re-scale/merge the already-integrated reflections in the input <code class="docutils literal notranslate"><span class=pre >_process.h5</span></code> (no re-integration)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >calibration</span></code></p> <td><p>Determine the detector geometry from powder rings; writes <code class="docutils literal notranslate"><span class=pre >&lt;prefix&gt;.poni</span></code></p> </table> <p>Calibration (<code class="docutils literal notranslate"><span class=pre >--mode</span> <span class=pre >calibration</span></code>):</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--calibrant</span> <span class=pre >&lt;name&gt;</span></code></p> <td><p>Powder standard: <code class="docutils literal notranslate"><span class=pre >lab6</span></code> | <code class="docutils literal notranslate"><span class=pre >agbh</span></code> | <code class="docutils literal notranslate"><span class=pre >ceo2</span></code> | <code class="docutils literal notranslate"><span class=pre >si</span></code> | <code class="docutils literal notranslate"><span class=pre >ice</span></code> (default <code class="docutils literal notranslate"><span class=pre >lab6</span></code>, case-insensitive)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--calibration</span> <span class=pre >&lt;txt&gt;</span></code></p> <td><p>How the rings are measured: <code class="docutils literal notranslate"><span class=pre >rings</span></code> | <code class="docutils literal notranslate"><span class=pre >spots</span></code> (default <code class="docutils literal notranslate"><span class=pre >rings</span></code>; see above). <code class="docutils literal notranslate"><span class=pre >rings</span></code> defaults <code class="docutils literal notranslate"><span class=pre >--azim-phi-bins</span></code> to 32</p> </table> <p>Detector mask:</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--detect-beam-stop[=N|off]</span></code></p> <td><p>Find the beam stop and its holder in a projection of N images and add them to the pixel mask as bit 9, so nothing shadowed by them is integrated. <strong>On by default</strong> (60 images); <code class="docutils literal notranslate"><span class=pre >=off</span></code> disables. Reflections behind the stop are attenuated but not flagged, so they integrate low with a plausible sigma and no existing rejection catches them</p> </table> <p>Geometry:</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--estimate-beam-center</span></code></p> <td><p>Measure the direct beam before indexing, from the symmetry of the spots where the sweep reaches at least half a turn and from the radial background profile where it does not; the value in the file is kept where neither can measure it. Off by default</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--no-fit-spindle</span></code></p> <td><p>With the above, keep the rotation axis given in the file instead of fitting its skew about the beam</p> </table> <p>Spot finding:</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--spot-sigma</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Noise sigma level for spot finding (default: 4.0)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--spot-threshold</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Photon-count threshold for spot finding (default: 10)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--adaptive-spots</span></code></p> <td><p>Self-calibrating detection (<strong>default</strong>, stills and rotation alike): the strong-pixel threshold comes from each image’s own per-resolution-ring noise instead of the fixed <code class="docutils literal notranslate"><span class=pre >--spot-threshold</span></code>, so one setting adapts across datasets (no per-dataset <code class="docutils literal notranslate"><span class=pre >--spot-threshold</span></code>/<code class="docutils literal notranslate"><span class=pre >--spot-sigma</span></code> tuning)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--no-adaptive-spots</span></code></p> <td><p>Turn adaptive detection off and use the fixed <code class="docutils literal notranslate"><span class=pre >--spot-threshold</span></code> / <code class="docutils literal notranslate"><span class=pre >--spot-sigma</span></code> finder</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--spot-false-pixels</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Adaptive-detection operating point: expected noise pixels tolerated per frame (default: 100; implies <code class="docutils literal notranslate"><span class=pre >--adaptive-spots</span></code>)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--spot-high-resolution</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>High-resolution limit for spot finding, Å. Omitted (or 0): no resolution clipping — spot finding extends as far as the detector reaches, for rotation data as well as stills</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--spot-low-resolution</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Low-resolution limit for spot finding, Å (default: 50; lower it, e.g. 24, to exclude the direct-beam halo on weak serial data; 0 removes the limit)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--min-pix-per-spot</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Minimum connected strong pixels per spot. <strong>If omitted, min-pix is chosen per image</strong> (stills indexing): the frame is indexed at min-pix 3/2/1 and the one maximising indexed-spot count × indexed fraction is kept. Give an explicit value to force a fixed min-pix instead.</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--max-spots</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Maximum spots kept per image (the strongest ones) and handed to indexing (default: 1000)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--detect-ice-rings[=on|off]</span></code></p> <td><p>Flag ice-ring spots (de-prioritised in indexing) and exclude ice-ring reflections from scaling. Default: the master file’s <code class="docutils literal notranslate"><span class=pre >detect_ice_rings</span></code>, or — where the file carries no such key — <strong>on for rotation and off for stills</strong></p> </table> <p>Azimuthal integration (the radial profile behind the per-image ice-ring score):</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >-q,</span> <span class=pre >--azim-q-spacing</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Q bin spacing, 1/Å (default: 0.01; finer resolves the narrow ice rings)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--azim-min-q</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Minimum Q, 1/Å</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--azim-max-q</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Maximum Q, 1/Å. Omitted: integration extends to the highest Q the detector reaches. The adaptive spot finder shares these Q bins, so this also sets how far self-calibrating detection can see</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--azim-phi-bins</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Number of azimuthal (phi) bins (default: 1)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--polarization-correction</span> <span class=pre >&lt;on|off&gt;</span></code></p> <td><p>Enable/disable the azimuthal polarization correction</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--solid-angle-correction</span> <span class=pre >&lt;on|off&gt;</span></code></p> <td><p>Enable/disable the azimuthal solid-angle correction</p> </table> <p>Indexing:</p> <p>A dataset with a <strong>rotation goniometer axis</strong> is processed as rotation data (two-pass rotation indexing) by default; a dataset without one is processed as independent stills. <code class="docutils literal notranslate"><span class=pre >--force-still</span></code> overrides the former; the <code class="docutils literal notranslate"><span class=pre >-R</span></code> / <code class="docutils literal notranslate"><span class=pre >--single-pass-rotation</span></code> / <code class="docutils literal notranslate"><span class=pre >--force-rotation-lattice</span></code> flags request rotation explicitly and pick the pass or lattice.</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--force-still</span></code></p> <td><p>Treat a rotation (goniometer) dataset as independent stills instead of rotation</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-X,</span> <span class=pre >--indexing-algorithm</span> <span class=pre >&lt;txt&gt;</span></code></p> <td><p><code class="docutils literal notranslate"><span class=pre >FFBIDX</span></code> | <code class="docutils literal notranslate"><span class=pre >FFT</span></code> | <code class="docutils literal notranslate"><span class=pre >FFTW</span></code> | <code class="docutils literal notranslate"><span class=pre >Auto</span></code> | <code class="docutils literal notranslate"><span class=pre >None</span></code></p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >-C,</span> <span class=pre >--unit-cell</span> <span class=pre >&lt;cell&gt;</span></code></p> <td><p>Reference unit cell <code class="docutils literal notranslate"><span class=pre >"a,b,c,alpha,beta,gamma"</span></code> (required by <code class="docutils literal notranslate"><span class=pre >ffbidx</span></code>)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-S,</span> <span class=pre >--space-group</span> <span class=pre >&lt;num|symbol&gt;</span></code></p> <td><p>Space group number (<code class="docutils literal notranslate"><span class=pre >92</span></code>) or Hermann-Mauguin symbol (<code class="docutils literal notranslate"><span class=pre >P43212</span></code>) — for indexing and scaling</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >-r,</span> <span class=pre >--refine</span> <span class=pre >&lt;txt&gt;</span></code></p> <td><p>Geometry refinement: <code class="docutils literal notranslate"><span class=pre >none</span></code> | <code class="docutils literal notranslate"><span class=pre >orientation</span></code> | <code class="docutils literal notranslate"><span class=pre >beam_and_lattice</span></code> (default) | <code class="docutils literal notranslate"><span class=pre >flex</span></code> (try all three per image, keep whichever indexes the most spots; alias <code class="docutils literal notranslate"><span class=pre >multi</span></code>)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-R,</span> <span class=pre >--two-pass-rotation[=num]</span></code></p> <td><p>Two-pass offline rotation indexing (default for goniometer data; optional first-pass image count, default 100)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--single-pass-rotation[=num]</span></code></p> <td><p>Online-like single-pass rotation indexing (optional min angular range, deg)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--force-rotation-lattice</span> <span class=pre >&lt;vec&gt;</span></code></p> <td><p>Force rotation lattice (9 floats, Å), skipping the first pass</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--rotation-no-postrefine</span></code></p> <td><p>Rotation: disable the default-on two-pass geometry post-refine (see the rotation section)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--refine-geometry[=N|off]</span></code></p> <td><p>Stills: extra first pass that bundle-adjusts the shared beam/distance/cell from N strongly-indexed frames (default 200) then re-indexes; default ON for stills with a reference cell (<code class="docutils literal notranslate"><span class=pre >-C</span></code> / <code class="docutils literal notranslate"><span class=pre >-z</span></code>), <code class="docutils literal notranslate"><span class=pre >=off</span></code> disables</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--index-ice-rings[=on|off]</span></code></p> <td><p>Index on the spots flagged as sitting on an ice ring too, instead of setting them aside (default: <strong>off</strong>; no effect without <code class="docutils literal notranslate"><span class=pre >--detect-ice-rings</span></code>, which does the flagging)</p> </table> <p>Indexer choice in brief: <code class="docutils literal notranslate"><span class=pre >ffbidx</span></code> (GPU) refines toward a <strong>known cell</strong> and is best for sparse serial stills; <code class="docutils literal notranslate"><span class=pre >fft</span></code> (GPU) / <code class="docutils literal notranslate"><span class=pre >fftw</span></code> (CPU) index <strong>de novo</strong> and suit strong rotation data. See the <a class="reference internal" href=CPU_DATA_ANALYSIS.html ><span class="std std-doc">CPU/GPU data-analysis reference</span></a> for the algorithms.</p> <p>Scaling and merging:</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--no-merge</span></code></p> <td><p>Skip scaling and merging (on by default); write only the per-image <code class="docutils literal notranslate"><span class=pre >_process.h5</span></code></p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-A,</span> <span class=pre >--anomalous</span></code></p> <td><p>Anomalous mode (keep Friedel pairs separate)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--scale-fulls</span></code> / <code class="docutils literal notranslate"><span class=pre >--no-scale-fulls</span></code></p> <td><p>rot3d: refit a per-frame scale on the combined fulls (XDS order, Unity model); on by default for rotation data, off for stills</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--smooth-g[=deg]</span></code></p> <td><p>rot3d: smooth the per-frame scale <em>G</em> over a degree range before the 3D combine (XDS DELPHI-like; default 5° for rotation, 0 = off)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--no-scaling-corrections</span></code></p> <td><p>rot3d: disable the default-on decay + absorption + modulation correction surfaces fitted on the fulls after scale-fulls (see below)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--relative-b[=deg]</span></code></p> <td><p>rot3d: fit a per-batch relative-<em>B</em> beyond the single decay slope over deg-degree batches, cross-validated (default 10° when bare; off otherwise)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--simple-stills</span></code></p> <td><p>Stills: treat every reflection as a full (<em>p</em> = 1, single-pass scale/merge) — disables the default-on physical partiality post-refinement</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--no-expected-variance-merge</span></code></p> <td><p>Stills: disable the default expected-variance merge weighting (which rebuilds each weak observation’s signal variance at the reflection mean to de-bias the inverse-variance merge); restores observed-sigma weighting</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--capture-uncertainty</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>rot3d: systematic sigma on under-captured fulls, ~num·(1−captured_fraction)·I (default: 1.0 for rotation, 0 otherwise)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--min-captured-fraction</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>rot3d: drop a combined full whose rocking curve was captured below this fraction — edge-of-sweep truncated fulls (default: 0.7 for rotation, 0 otherwise; 0 = off)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--scaling-high-resolution</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>High-resolution limit for scaling, Å — manual override (default: no limit; disables the automatic cutoff below)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--scaling-low-resolution</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Low-resolution limit for scaling and merging, Å (default: 50, the value XDS configurations use; 0 removes the limit). Reflections coarser than this sit behind or beside the beam stop and are measured on a background it has eaten into</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--resolution-cutoff</span> <span class=pre >&lt;txt&gt;</span></code></p> <td><p>Automatic high-resolution cutoff for the written reflections and reported shells: <code class="docutils literal notranslate"><span class=pre >cc-logistic</span></code> | <code class="docutils literal notranslate"><span class=pre >off</span></code> (default: <code class="docutils literal notranslate"><span class=pre >cc-logistic</span></code>; ignored when <code class="docutils literal notranslate"><span class=pre >--scaling-high-resolution</span></code> is set)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--resolution-cc-target</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>CC1/2 target defining the <code class="docutils literal notranslate"><span class=pre >cc-logistic</span></code> fall-off (default: 0.30)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--resolution-shells</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Number of resolution shells in the reported statistics table (default: 10)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--min-partiality</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Minimum partiality to accept a reflection (default: 0.02)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--ice-min-score</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Ice-presence gate: the measured per-run ice score (1 = no ice) a dataset must reach before <strong>any</strong> ice handling is applied — the flagging and the exclusion from scaling (default: 1.5; 0 = no gate). The eleven fixed hexagonal bands cover 16–26 % of the unique reflections whether or not the crystal has ice, so handling ice on a clean crystal only costs completeness</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--ice-min-spot-ratio</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>The second ice-presence channel: found <strong>spots</strong> on the hexagonal rings over the same q width of ice-free flanks beside them (1 = spots spread evenly). Ice in large crystallites diffracts as discrete spots and leaves the radial profile flat, so <code class="docutils literal notranslate"><span class=pre >--ice-min-score</span></code> alone is blind to it (default: 2.0; 0 disables this channel)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--reject-outliers</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Per-observation outlier rejection, N σ from the per-reflection median (default: 6 for <code class="docutils literal notranslate"><span class=pre >rot3d</span></code>, off otherwise)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--min-image-cc</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Per-image CC limit, percent (default: no limit)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--search-min-zeta</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>De-novo space-group search only: also search a merge of just the observations whose Lorentz geometry |ζ| reaches this, and report both answers (default: 0.85 for rotation, 0 = single search). Reflections crossing the Ewald sphere near-tangentially are measured worst and can make a real symmetry operator look like a twin law. Where the two searches disagree, the merge of all the observations decides — as it always has for the systematic absences</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--mosaicity</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Diagnostic: fix the scaling mosaicity (°) instead of using the per-image seed</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--scaling-iterations</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Scaling iterations with no reference data (default: 3)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >-z,</span> <span class=pre >--reference-mtz</span> <span class=pre >&lt;file&gt;</span></code></p> <td><p>Reference MTZ (enables reference-driven scaling)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--reference-column</span> <span class=pre >&lt;label&gt;</span></code></p> <td><p>Reference MTZ column to use (default: auto — F-model, else IMEAN/I/…)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--model</span> <span class=pre >&lt;file.pdb&gt;</span></code></p> <td><p>After merging, validate the merged intensities against this atomic model (see below)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--write-process-h5</span></code></p> <td><p>Also write the (large) <code class="docutils literal notranslate"><span class=pre >_process.h5</span></code> when merging (default: only <code class="docutils literal notranslate"><span class=pre >.mtz</span></code>/<code class="docutils literal notranslate"><span class=pre >.cif</span></code>)</p> </table> <p>Integration:</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--integrator</span> <span class=pre >&lt;txt&gt;</span></code></p> <td><p>Spot integrator: <code class="docutils literal notranslate"><span class=pre >gaussian</span></code> (profile-fit, default) | <code class="docutils literal notranslate"><span class=pre >empirical</span></code> | <code class="docutils literal notranslate"><span class=pre >boxsum</span></code> (classical fallback)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--integration-radius</span> <span class=pre >&lt;r&gt;</span></code></p> <td><p>Signal-box radius <code class="docutils literal notranslate"><span class=pre >r1</span></code>, or <code class="docutils literal notranslate"><span class=pre >r1,r2,r3</span></code> (px). One value ⇒ <code class="docutils literal notranslate"><span class=pre >r2=r1+2</span></code>, <code class="docutils literal notranslate"><span class=pre >r3=r1+4</span></code></p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--integration-stencil</span> <span class=pre >&lt;k&gt;</span></code></p> <td><p>Push the <code class="docutils literal notranslate"><span class=pre >r2..r3</span></code> background ring out by <code class="docutils literal notranslate"><span class=pre >k</span></code> times the beam’s radial streak <code class="docutils literal notranslate"><span class=pre >bandwidth·R_px</span></code>, per reflection (default <code class="docutils literal notranslate"><span class=pre >0</span></code> = the fixed circular ring). A fixed ring otherwise ends up on a streaked reflection’s own tails at high resolution and measures them as background. Only the ring moves, and only radially — the <code class="docutils literal notranslate"><span class=pre >r1</span></code> signal box stays a circle — and the growth is capped at <code class="docutils literal notranslate"><span class=pre >2·r3</span></code>. The neighbour exclusion grows with it, so on a crowded pattern a few reflections can be left with too little background and dropped. Needs <code class="docutils literal notranslate"><span class=pre >--bandwidth</span></code>: on a monochromatic beam the streak is zero and this does nothing</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--background-clip</span> <span class=pre >&lt;n&gt;</span></code></p> <td><p>Monochromatic (rotation + still): high-side clip of the background ring at <code class="docutils literal notranslate"><span class=pre >mean</span> <span class=pre >+</span> <span class=pre >n·√mean</span></code> (default 4; 0 = off). The default background estimator — it rejects neighbour cores and zingers without the symmetric trim’s Poisson skew bias. Broadband data always clip, at 3σ; ignored by <code class="docutils literal notranslate"><span class=pre >--integrator</span> <span class=pre >boxsum</span></code></p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--background-trim</span> <span class=pre >&lt;f&gt;</span></code></p> <td><p>Use the old symmetric trimmed mean for the background ring instead of the clip, 0≤f&lt;0.5 (<code class="docutils literal notranslate"><span class=pre >0.10</span></code> was the former default). Switches <code class="docutils literal notranslate"><span class=pre >--background-clip</span></code> off. A symmetric trim is biased low on Poisson data and adds ~5 counts to every partial, so this is for back compatibility only; <code class="docutils literal notranslate"><span class=pre >0</span></code> = plain ring mean. Rings holding more than 512 pixels fall back to the plain mean (the GPU sorts the ring in shared memory and the CPU now matches it), which the default radii never reach but wide ones do</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--background-radial[=on|off|auto]</span></code></p> <td><p>Correct the background ring for the <strong>curvature</strong> of the radial background (default <strong>off</strong>). Disk and ring are concentric, so a background linear in position cancels between them and only curvature survives — which on a smooth ice ring reaches +26 counts on a single reflection. <code class="docutils literal notranslate"><span class=pre >auto</span></code> applies it per image where that image’s ice score shows a <em>smooth</em> powder ring, since the model is a function of radius alone: on ice made of discrete crystallite spots there is no smooth ring and the correction makes the bias worse. Ignored by <code class="docutils literal notranslate"><span class=pre >--integrator</span> <span class=pre >boxsum</span></code> (no clip pass to take the curve from)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--integration-high-resolution</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>High-resolution limit for prediction and integration. Omitted (or 0) means integration extends as far as the detector reaches — which is what the predictor can place on the detector anyway, since it rejects reflections that miss it. Set a value to integrate less than the detector offers</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--max-hkl</span> <span class=pre >&lt;n&gt;</span></code></p> <td><p>Predict reflections with |h|,|k|,|l| ≤ <code class="docutils literal notranslate"><span class=pre >n</span></code> (max 511). By default this is derived per crystal from the refined cell as <code class="docutils literal notranslate"><span class=pre >ceil(max(a,b,c)/d_min)</span> <span class=pre >+</span> <span class=pre >1</span></code>, which is the exact bound: the predictor keeps only |q| ≤ 1/d_min and <code class="docutils literal notranslate"><span class=pre >h</span> <span class=pre >=</span> <span class=pre >a·q</span></code>, so no reflection can lie outside it and no candidate inside it is wasted on a shorter axis. Set it only to override that</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--bandwidth</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Relative X-ray bandwidth FWHM (e.g. <code class="docutils literal notranslate"><span class=pre >0.01</span></code> for a 1% DMM); default from file or 0 (monochromatic)</p> </table> <p>Geometry overrides (defaults are taken from the input file; override them to reprocess with a corrected geometry):</p> <table> <thead> <tr class=row-odd ><th class=head ><p>Option</p> <th class=head ><p>Description</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--beam-x</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Beam centre X (pixel)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--beam-y</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Beam centre Y (pixel)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--detector-distance</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Detector distance (mm)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--wavelength</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Wavelength (Å)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--rot1</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>PONI detector rotation 1 (rad)</p> <tr class=row-odd ><td><p><code class="docutils literal notranslate"><span class=pre >--rot2</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>PONI detector rotation 2 (rad)</p> <tr class=row-even ><td><p><code class="docutils literal notranslate"><span class=pre >--polarization</span> <span class=pre >&lt;num&gt;</span></code></p> <td><p>Polarization factor</p> </table> </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=JFJOCH_WRITER.html title=jfjoch_writer 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> jfjoch_writer </span> </div> </a> <a href=JFJOCH_VIEWER.html title=jfjoch_viewer 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> jfjoch_viewer </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>
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