From f4620470383572c5c67f1dd8dc90d5437b34ea25 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Fri, 9 Oct 2026 17:07:22 +0200 Subject: [PATCH] rugnux report: BEAM_CENTRE_OFF warning when the file's beam centre is wrong The pre-scan's beam-centre check and the post-refinement both measure where the direct beam lands, but the report only carried the centre the run used. Section 1 now sets the file's direct beam (FILE_DIRECT_BEAM) beside the background's (BACKGROUND_DIRECT_BEAM, with its sigma), the shift of the refined centre from the file's (BEAM_CENTRE_SHIFT) and the tolerance the geometry asks for (BEAM_CENTRE_TOLERANCE: BeamCenterNeed_pxl, the number the log's check prints, here on the run's own cell). A shift above the tolerance is a BEAM_CENTRE_OFF warning naming the file's, refined and background centres, the difference in px and mm and the value to correct the beamline to; a run that refined no centre is warned on the background alone where its fit resolves the difference (3 sigma). The summary gains a Beam centre line. The refined centre, not the background, is the trigger wherever one exists: on a battery set where XDS's refined direct beam and rugnux's agree to 1 px, the background fit is 12 px away from both. Report-only; no result changes. Co-Authored-By: Claude Opus 5.5 (1M context) Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi --- docs/RUGNUX_REPORT.md | 26 +++++++++++++-- rugnux/ReportDocument.h | 1 + rugnux/ResultReport.cpp | 67 ++++++++++++++++++++++++++++++++++++++ rugnux/Rugnux.cpp | 9 +++++ rugnux/Rugnux.h | 7 ++++ tests/ResultReportTest.cpp | 36 ++++++++++++++++++++ 6 files changed, 144 insertions(+), 2 deletions(-) diff --git a/docs/RUGNUX_REPORT.md b/docs/RUGNUX_REPORT.md index ffaacd498..63e73672d 100644 --- a/docs/RUGNUX_REPORT.md +++ b/docs/RUGNUX_REPORT.md @@ -128,6 +128,28 @@ JFJOCH_DATASET_SETTINGS= {"beam_x_pxl": 2078.24, "beam_y_pxl": 2233.92, "detecto grep '^JFJOCH_DATASET_SETTINGS=' out_report.txt | cut -d' ' -f2- > geometry.json ``` +**The beam centre in the file.** Section 1 sets the file's centre beside the two the run measured: +**`FILE_DIRECT_BEAM=`** is where the input file puts the direct beam (its beam centre, under its own +detector tilt), **`BACKGROUND_DIRECT_BEAM=`** where the scattered background puts it, with the fit's +sigma (the pre-scan's beam-centre check), and **`BEAM_CENTRE_SHIFT=`** how far the centre the result was +integrated at (`DIRECT_BEAM=`, the refined one on a rotation run) lies from the file's, in pixels. +**`BEAM_CENTRE_TOLERANCE=`** is how far this crystal on this geometry lets the centre be wrong - the +displacement at which the accumulated reflections of the longest cell axis smear to 70% of their +height, the number the log's `Beam centre check` line states, here on the run's own cell. Where the +shift is larger, a **`BEAM_CENTRE_OFF`** warning gives the file's, the refined and the background +centre, the difference in pixels and millimetres, and the value to correct the beamline (or the +header) to: the run itself integrated at the refined centre, but every other program given the same +file starts from the wrong one. A run that refined no centre (stills) is warned on the background +alone, where its fit resolves the difference (three sigma) and the difference exceeds the tolerance, +worded as a check. The summary's `Beam centre` line states the outcome either way. + +``` +FILE_DIRECT_BEAM= 1564.31 1702.91 +BACKGROUND_DIRECT_BEAM= 1571.30 1699.85 0.62 +BEAM_CENTRE_SHIFT= 7.15 +BEAM_CENTRE_TOLERANCE= 3.49 +``` + **Which pass.** A rotation run integrates twice — once at the geometry in the input file (the first half of the sweep but at least 120°, `--prepass-fraction`), then the whole sweep again at the post-refined geometry — and can integrate a third time if a guard rejects the second pass. There is **one** report, for the pass that became the canonical output, and `PASS=` / @@ -156,13 +178,13 @@ and a run that produced a textbook data set read identically for their first thr `GONIO_SCALE`, `SPINDLE_CAP`, `ANISOTROPY`, `TWINNING`, `PSEUDO_TRANSLATION`, `LATTICE_TRANSLATION`, `MODEL_HAND`, `MODEL_NOT_VALIDATED`, `REFERENCE_MISMATCH`, `CANCELLED`, `RESOLUTION_FIT`, `FLIGHT_PATH`, `GEOMETRY_NOT_CONVERGED`, `SCALING_NOT_CONVERGED`, `HARMONIC_CONTAMINATION`, - `SUPERCELL_POSSIBLE`, `MULTIPLE_LATTICES`, `ICE_RINGS`, `POWDER_RINGS`. `NONE` when nothing fired. A code appears if and only if its + `SUPERCELL_POSSIBLE`, `MULTIPLE_LATTICES`, `ICE_RINGS`, `POWDER_RINGS`, `BEAM_CENTRE_OFF`. `NONE` when nothing fired. A code appears if and only if its warning fired, so the flags and the `WARNING:` lines are two renderings of one list. Thresholds are deliberately low: a warning is a prompt to check something, not a verdict, and some of them fire on data that turn out fine — the closed type for machinery, the open sentence for a person. - Below them, one line each, the facts a reader needs before reading further: space group, cell, - mosaicity, the powder and ice rings, multiple lattices, resolution, completeness, signal, anomalous + mosaicity, the beam centre, the powder and ice rings, multiple lattices, resolution, completeness, signal, anomalous signal, anisotropy, pseudo-symmetry, twinning, supercell, radiation damage and the sweep. A line states a finding that is not a condition too - weak powder rings, a possible supercell no stronger than correct cells show, an arbitrary indexing choice (`Indexing choice`, a rotation sweep whose cell diff --git a/rugnux/ReportDocument.h b/rugnux/ReportDocument.h index eeee5e620..5f1361317 100644 --- a/rugnux/ReportDocument.h +++ b/rugnux/ReportDocument.h @@ -51,6 +51,7 @@ namespace PathologyCode { constexpr const char *SCALING_NOT_CONVERGED = "SCALING_NOT_CONVERGED"; // the per-frame scales hit their cap still moving constexpr const char *POWDER_RINGS = "POWDER_RINGS"; // non-ice powder rings hold many spots constexpr const char *ICE_RINGS = "ICE_RINGS"; // hexagonal-ice rings hold many spots + constexpr const char *BEAM_CENTRE_OFF = "BEAM_CENTRE_OFF"; // the file's beam centre is wrong for this geometry } // A closed type plus an open description. The type is what machinery switches on; the text is what a diff --git a/rugnux/ResultReport.cpp b/rugnux/ResultReport.cpp index 7a752dae1..48b8847c7 100644 --- a/rugnux/ResultReport.cpp +++ b/rugnux/ResultReport.cpp @@ -42,6 +42,8 @@ namespace { // UNDECLARED_LATTICE_TRANSLATION_PCT and INDEXING_AMBIGUITY_OPERATORS; INDEXING_RATE is a // --developer key on rotation runs; POWDER_ICE_* / POWDER_NON_ICE_SPOT_FRACTION; // the ICE_RINGS and POWDER_RINGS flags. + // 16: FILE_DIRECT_BEAM / BACKGROUND_DIRECT_BEAM / BEAM_CENTRE_SHIFT / BEAM_CENTRE_TOLERANCE in + // section 1 and the BEAM_CENTRE_OFF flag - the file's beam centre against the refined one. // 8: every line that is not `KEY= value` and not blank starts with `#`, warnings included // (`# WARNING:`); the header gains RUGNUX_DOWNLOAD and BUILD_CXX_FLAGS, and RUGNUX_GIT is // the full build-time hash. @@ -408,6 +410,8 @@ ReportDocument BuildReportDocument(const std::string &output_prefix, const bool rotation = experiment.IsRotationIndexing(); const bool merged = result.has_merge_statistics; doc.warnings = result.warnings; + // SUMMARY rows filled by the sections that measure them; empty leaves the row out. + std::string beam_centre_row; // ------------------------------------------------------------------ header block { @@ -543,6 +547,67 @@ ReportDocument BuildReportDocument(const std::string &output_prefix, "integrated at is the best one reached, not a settled one (see PASS_DECISION)"); } + // The beam centre against the file's. The file's is read off the experiment the run was + // given - the header, with the header's tilt - and compared with where the result was + // integrated (the refined geometry) and with where the scattered background put the beam. The + // run corrects a wrong centre for itself; every other program reading the same file does not, + // which is why this is worth a warning however well the run went. The tolerance is the one the + // pre-scan's check prints (BeamCenterNeed_pxl), taken on the run's own cell. + { + const auto file_direct = experiment.GetDiffractionGeometry().GetDirectBeam_pxl(); + const double pixel_mm = experiment.GetPixelSize_mm(); + const double need = result.beam_centre_need_pxl; + const double moved = std::hypot(result.used_direct_beam_x_pxl - file_direct.first, + result.used_direct_beam_y_pxl - file_direct.second); + const auto &bg = result.background_beam_centre; + const double bg_moved = bg ? std::hypot(bg->beam_x_pxl - file_direct.first, + bg->beam_y_pxl - file_direct.second) : NAN; + Add(s, KeyText("FILE_DIRECT_BEAM", fmt::format("{:.2f} {:.2f}", file_direct.first, + file_direct.second))); + if (bg) + Add(s, KeyText("BACKGROUND_DIRECT_BEAM", fmt::format("{:.2f} {:.2f} {:.2f}", bg->beam_x_pxl, + bg->beam_y_pxl, bg->sigma_pxl))); + Add(s, KeyReal("BEAM_CENTRE_SHIFT", moved, "{:.2f}")); + if (std::isfinite(need)) + Add(s, KeyReal("BEAM_CENTRE_TOLERANCE", need, "{:.2f}")); + // The refined geometry is the evidence wherever the run refined one: the background fit can + // be pulled by an asymmetric background, and where both exist and disagree the spot + // positions are what the result rests on. Only a run that refined nothing (stills, no + // post-refinement) is warned on the background alone, and only where the fit resolves the + // difference at all (three of its own sigma, as the pre-scan's check reads it). + const bool bg_resolves = bg && bg_moved > 3.0 * bg->sigma_pxl; + const std::string bg_text = bg ? fmt::format("the scattered background at ({:.2f}, {:.2f}) +- {:.2f} px", + bg->beam_x_pxl, bg->beam_y_pxl, bg->sigma_pxl) + : std::string(); + if (std::isfinite(need) && moved > need) { + beam_centre_row = fmt::format("the file's is OFF by {:.1f} px ({:.2f} mm) - correct the " + "beamline value", moved, moved * pixel_mm); + Warn(doc, PathologyCode::BEAM_CENTRE_OFF, fmt::format( + "the beam centre in the input file is {:.1f} px ({:.2f} mm) from where this run found " + "the direct beam, more than the {:.1f} px this geometry needs it to be right to: the " + "file puts the direct beam at ({:.2f}, {:.2f}), the refined geometry at ({:.2f}, " + "{:.2f}){}. This run used the refined centre, but any other program given this file " + "starts from the wrong one - correct the beam centre at the beamline (or in the " + "file's header) to ({:.2f}, {:.2f})", + moved, moved * pixel_mm, need, file_direct.first, file_direct.second, + result.used_direct_beam_x_pxl, result.used_direct_beam_y_pxl, + bg ? ", " + bg_text : std::string(), + result.used_direct_beam_x_pxl, result.used_direct_beam_y_pxl)); + } else if (std::isfinite(need) && !result.post_refine && bg_resolves && bg_moved > need) { + beam_centre_row = fmt::format("the background puts it {:.1f} px ({:.2f} mm) from the file's - " + "check the beamline value", bg_moved, bg_moved * pixel_mm); + Warn(doc, PathologyCode::BEAM_CENTRE_OFF, fmt::format( + "the beam centre in the input file may be off: the file puts the direct beam at " + "({:.2f}, {:.2f}), {} - {:.1f} px ({:.2f} mm) away, more than the {:.1f} px this " + "geometry needs the centre to be right to. Nothing on this run refined the centre, so " + "this is the background's word alone: check the beam centre at the beamline and " + "correct it if this is confirmed", + file_direct.first, file_direct.second, bg_text, bg_moved, bg_moved * pixel_mm, need)); + } else if (std::isfinite(need)) + beam_centre_row = fmt::format("the file's is within the {:.1f} px this geometry needs ({:.1f} px " + "from the refined one)", need, moved); + } + Add(s, Blank()); // Where the geometry came from. This is the whole provenance story a user needs, because a // user acts on exactly one geometry: the one the result was produced with. @@ -2377,6 +2442,8 @@ ReportDocument BuildReportDocument(const std::string &output_prefix, row("Indexing choice", fmt::format("alternative indexing {} - one sweep is indexed consistently, " "so it matters only against other data: index against those " "with -z or --model", result.indexing_ambiguity_operators)); + if (!beam_centre_row.empty()) + checked_row("Beam centre", {PathologyCode::BEAM_CENTRE_OFF}, beam_centre_row); if (!result.powder.rings_q_recipA.empty() || result.consensus_cell) { const auto &pw = result.powder; checked_row("Powder", {PathologyCode::POWDER_RINGS}, pw.rings_q_recipA.empty() ? std::string("no rings detected") diff --git a/rugnux/Rugnux.cpp b/rugnux/Rugnux.cpp index 804f78bdd..bfa4dd921 100644 --- a/rugnux/Rugnux.cpp +++ b/rugnux/Rugnux.cpp @@ -434,8 +434,17 @@ ProcessResult Rugnux::Run(RugnuxObserver *observer) { // on the rotation two-pass that is under a third of what the run actually took, the pre-scan and the // first pass being invisible in it. Time the whole thing here, where every pass is inside. const auto run_start = std::chrono::steady_clock::now(); + DiffractionExperiment header_experiment = experiment_; ProcessResult result = RunAllPasses(observer); result.total_time_s = std::chrono::duration(std::chrono::steady_clock::now() - run_start).count(); + // For the report's beam-centre warning: what the background measured, and what this crystal asks + // of the centre - at the file's geometry, as the pre-scan's check asks it, but on the cell the run + // determined rather than the long axis that check has to assume. + JoinBeamCenterCapture(); + result.background_beam_centre = measured_beam_center_; + if (result.consensus_cell) + header_experiment.SetUnitCell(*result.consensus_cell); + result.beam_centre_need_pxl = BeamCenterNeed_pxl(header_experiment); return result; } diff --git a/rugnux/Rugnux.h b/rugnux/Rugnux.h index 4df80b6b8..2c8068da2 100644 --- a/rugnux/Rugnux.h +++ b/rugnux/Rugnux.h @@ -530,6 +530,13 @@ struct ProcessResult { // did not post-refine (stills, single pass, or the refinement did not converge). std::optional post_refine; + // The beam centre the scattered background puts the direct beam at (the pre-scan's check), and + // how far the centre may be wrong on this crystal (BeamCenterNeed_pxl, with the run's cell where + // it has one). Report only: the file's centre is read off the experiment the report is given, the + // refined one off used_direct_beam_*. Empty / NaN where the check did not run. + std::optional background_beam_centre; + float beam_centre_need_pxl = NAN; + // Which pass this result is (1-based) and how many ran, plus one line saying which pass became the // canonical output and on what evidence. pass_count == 1 outside the rotation two-pass. int pass_number = 1; diff --git a/tests/ResultReportTest.cpp b/tests/ResultReportTest.cpp index 1f964ed5c..010930e83 100644 --- a/tests/ResultReportTest.cpp +++ b/tests/ResultReportTest.cpp @@ -1200,3 +1200,39 @@ TEST_CASE("ResultReport_Checks", "[Diagnostics]") { CHECK(std::ranges::any_of(c.codes, [&](const std::string &code) { return std::ranges::find(doc.pathology_flags, code) != doc.pathology_flags.end(); })); } + +TEST_CASE("ResultReport_BeamCentreOff", "[Diagnostics]") { + DiffractionExperiment x(DetJF(1)); + x.BeamX_pxl(500.0f).BeamY_pxl(400.0f); + const auto file = x.GetDiffractionGeometry().GetDirectBeam_pxl(); + ProcessResult result; + result.post_refine = PostRefineResult{}; + result.beam_centre_need_pxl = 2.0f; + result.background_beam_centre = BeamCenterEstimate{.beam_x_pxl = static_cast(file.first) + 5.0f, + .beam_y_pxl = static_cast(file.second), + .sigma_pxl = 0.5f}; + + // Refined within the tolerance: the background's word is not enough where the centre was refined. + result.used_direct_beam_x_pxl = file.first + 1.0; + result.used_direct_beam_y_pxl = file.second; + auto text = RenderResultReport("p", "in.h5", x, result); + CHECK(text.find("BEAM_CENTRE_OFF") == std::string::npos); + CHECK(text.find("\nBEAM_CENTRE_SHIFT= 1.00\n") != std::string::npos); + CHECK(text.find("\nBEAM_CENTRE_TOLERANCE= 2.00\n") != std::string::npos); + + // Refined 4 px off the file's centre: warned, with both centres, px and mm, and the advice. + result.used_direct_beam_x_pxl = file.first; + result.used_direct_beam_y_pxl = file.second + 4.0; + text = RenderResultReport("p", "in.h5", x, result); + CHECK(text.find("\nPATHOLOGY_FLAGS= BEAM_CENTRE_OFF\n") != std::string::npos); + CHECK(text.find("4.0 px (0.30 mm)") != std::string::npos); + CHECK(text.find("correct the beam centre at the beamline") != std::string::npos); + + // Nothing refined (stills): the background alone warns, worded as a check. + result.post_refine.reset(); + result.used_direct_beam_x_pxl = file.first; + result.used_direct_beam_y_pxl = file.second; + text = RenderResultReport("p", "in.h5", x, result); + CHECK(text.find("\nPATHOLOGY_FLAGS= BEAM_CENTRE_OFF\n") != std::string::npos); + CHECK(text.find("the background's word alone") != std::string::npos); +}