leonarski_fandClaude Opus 5
26fc4b02b3
The adopted space group travelled the pipeline as a bare int and was rebuilt downstream with find_spacegroup_by_number, which returns the reference setting. So every setting a number cannot name was destroyed one line after it was determined: P 1 1 2 came back as P 1 2 1, I 1 1 2 as C 1 2 1, R 3:R as R 3:H. DatasetSettings now holds the gemmi::SpaceGroup itself, DiffractionExperiment exposes it as GetGemmiSpaceGroup() / GetSpaceGroupOrP1(), and everything that used to take an int - HKLKeyGenerator (its int constructor is gone, so the compiler finds the callers), the merge, the R-free flags, French-Wilson, the reindexing ambiguity, the completeness enumeration, the MTZ and mmCIF exports, the model validation - takes the group. -S keeps the setting the symbol names rather than reducing it to a number. The end message carries both spellings and a reader prefers the name, since only the name keeps the setting while the number is what a reader written before the name understands. It carries them over CBOR too: the determined group was never serialised at all, so a group rugnux chose reached the master file only when the same process wrote it, and an online writer fell back to whatever the user had supplied at the start. Both keys are optional additions, so an older reader skips them and a newer one reads an older sender. On disk the master's /entry/sample/space_group carries the extended Hermann-Mauguin name and is what the reader takes the group from, so a setting survives a _process.h5 and the --mode scale that re-reads it; the number stays beside it and is the fallback for files written before. Every one of the 230 reference settings the old writer could produce reads back as itself, so older files are unaffected. Stage A and Stage B of the search still enumerate reference settings only, so this determines no group differently today - it is what the enumeration needs before it can be widened. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
469 lines
30 KiB
C++
469 lines
30 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <algorithm>
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#include <fstream>
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#include <sstream>
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#include <spdlog/fmt/fmt.h>
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#include "../common/GitInfo.h"
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#include "../common/time_utc.h"
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#include "../image_analysis/scale_merge/AnisotropyAnalysis.h"
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#include "../image_analysis/scale_merge/Merge.h"
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#include "../image_analysis/scale_merge/SearchSpaceGroup.h"
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#include "../image_analysis/scale_merge/TwinningAnalysis.h"
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#include "ResultReport.h"
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namespace {
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// The version of this file format. Bumped when a key is renamed or removed, a table column moves,
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// or a reason code changes meaning - a consumer can gate on it.
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constexpr int REPORT_VERSION = 4;
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const char *BANNER = " ******************************************************************************";
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void Section(std::ostream &os, const std::string &title) {
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os << "\n" << BANNER << "\n " << title << "\n" << BANNER << "\n\n";
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}
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// Every number a consumer might want is written as one of these, so it is one grep away.
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template <class T> void Key(std::ostream &os, const char *key, const T &value) {
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os << key << "= " << value << "\n";
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}
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std::string CellString(const UnitCell &c) {
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return fmt::format("{:.3f} {:.3f} {:.3f} {:.3f} {:.3f} {:.3f}", c.a, c.b, c.c,
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c.alpha, c.beta, c.gamma);
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}
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}
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std::string RenderResultReport(const std::string &output_prefix,
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const std::string &input_file,
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const DiffractionExperiment &experiment,
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const ProcessResult &result,
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const RunProvenance &provenance) {
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std::ostringstream os;
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const bool rotation = experiment.IsRotationIndexing();
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const bool merged = result.has_merge_statistics;
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std::vector<std::string> warnings = result.warnings;
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os << BANNER << "\n"
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<< " RUGNUX PROCESSING REPORT\n"
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<< BANNER << "\n\n"
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<< " What this run determined, written next to its other output. The `KEY= value` lines and\n"
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<< " the tables below are a stable interface - a script greps them, and REPORT_VERSION says\n"
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<< " when that interface last changed. Rates and per-image progress are not here; they are\n"
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<< " on stdout.\n\n";
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Key(os, "REPORT_VERSION", REPORT_VERSION);
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Key(os, "RUGNUX_VERSION", jfjoch_version());
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if (!jfjoch_git_sha1().empty())
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Key(os, "RUGNUX_GIT", jfjoch_git_sha1().substr(0, 6) + " " + jfjoch_git_date());
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Key(os, "DATE", time_UTC(std::chrono::system_clock::now()));
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Key(os, "INPUT_FILE", input_file);
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Key(os, "OUTPUT_PREFIX", output_prefix);
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// How the result was produced, what it cost and what it ran on, so the report stands on its own
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// once the shell history it came from is gone. Absent rather than zero where the caller does not
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// know them - the library and the viewer have no command line and no invocation to time.
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if (!provenance.command_line.empty())
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Key(os, "COMMAND_LINE", provenance.command_line);
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if (provenance.wall_time_s > 0.0)
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Key(os, "WALL_TIME", fmt::format("{:.2f}", provenance.wall_time_s));
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if (provenance.gpu_count >= 0) {
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Key(os, "GPU_COUNT", provenance.gpu_count);
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// GPU_COUNT= 0 with no GPU= line is the CPU-only case, and saying so is the point: whether
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// the GPUs were there is the first question about how long the run took.
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if (!provenance.gpu_description.empty())
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Key(os, "GPU", provenance.gpu_description);
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}
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// ---------------------------------------------------------------- 1. DATA SET
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Section(os, "1. DATA SET");
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Key(os, "EXPERIMENT_TYPE", rotation ? "ROTATION" : "STILLS");
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Key(os, "IMAGES_PROCESSED", result.images_processed);
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Key(os, "WAVELENGTH", fmt::format("{:.5f}", experiment.GetWavelength_A()));
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if (const auto gonio = experiment.GetGoniometer()) {
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Key(os, "OSCILLATION_RANGE", fmt::format("{:.4f}", gonio->GetIncrement_deg()));
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Key(os, "STARTING_ANGLE", fmt::format("{:.3f}", gonio->GetStart_deg()));
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const auto ax = gonio->GetAxis();
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Key(os, "ROTATION_AXIS", fmt::format("{:.6f} {:.6f} {:.6f}", ax.x, ax.y, ax.z));
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}
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Key(os, "DETECTOR_DISTANCE", fmt::format("{:.3f}", result.used_distance_mm));
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Key(os, "BEAM_CENTRE", fmt::format("{:.2f} {:.2f}", result.used_beam_x_pxl, result.used_beam_y_pxl));
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os << "\n"
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<< " The distance and beam centre above are the ones this result was integrated at, which on\n"
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<< " a rotation run is the post-refined geometry rather than the values in the input file.\n";
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// The same geometry once more, as the object jfjoch_broker takes it in: the four required
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// properties of dataset_settings in broker/jfjoch_api.yaml, spelled the way the API spells them.
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// A run that refined the geometry is usually the best measurement of it anyone has, and without
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// this the only way back into the instrument is to read two numbers off this report by eye and
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// retype them. One line, valid JSON, so a script can lift it with a grep and POST it.
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os << "\n";
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Key(os, "JFJOCH_DATASET_SETTINGS",
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fmt::format(R"({{"beam_x_pxl": {:.2f}, "beam_y_pxl": {:.2f}, "detector_distance_mm": {:.3f}, )"
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R"("incident_energy_keV": {:.4f}}})",
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result.used_beam_x_pxl, result.used_beam_y_pxl, result.used_distance_mm,
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experiment.GetDatasetSettings().GetPhotonEnergy_keV()));
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os << "\n"
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<< " The geometry above as jfjoch_broker's dataset_settings, to carry a refined beam centre and\n"
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<< " distance back to the instrument for the next collection.\n";
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if (result.spot_resolution_estimate_A.has_value()) {
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os << "\n";
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Key(os, "SPOT_RESOLUTION_ESTIMATE", fmt::format("{:.2f}", *result.spot_resolution_estimate_A));
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os << "\n"
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<< " How far the merged data are expected to reach, read off the found spots alone - no\n"
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<< " lattice, no integration, no merge. It is a prediction, good to about 0.2 A on the\n"
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<< " rotation data it was calibrated on, and it is not what the run achieved: compare it\n"
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<< " with INCLUDE_RESOLUTION_RANGE in section 5. It is not limited to what this detector\n"
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<< " records: where it reads finer than the high-resolution end of that range, the crystal\n"
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<< " diffracts past the corner and the run is detector-limited.\n";
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}
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if (result.pass_count > 1) {
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os << "\n";
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Key(os, "PASS", fmt::format("{} of {}", result.pass_number, result.pass_count));
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Key(os, "PASS_DECISION", result.pass_decision);
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os << "\n"
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<< " A rotation run integrates twice: once at the geometry in the input file, then again at\n"
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<< " the post-refined geometry. Every number in this report describes the pass named above,\n"
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<< " whose files are " << output_prefix << ".*; the header-geometry pass is not written.\n";
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}
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// ---------------------------------------------------------------- 2. INDEXING
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Section(os, "2. INDEXING");
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if (result.indexing_rate.has_value())
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Key(os, "INDEXING_RATE", fmt::format("{:.4f}", result.indexing_rate.value()));
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Key(os, "LATTICE_FOUND", (result.consensus_cell.has_value() ? "TRUE" : "FALSE"));
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if (result.consensus_cell.has_value())
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Key(os, "UNIT_CELL_CONSTANTS", CellString(*result.consensus_cell));
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if (result.space_group.has_value())
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Key(os, "SPACE_GROUP_NUMBER", result.space_group->number);
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if (result.indexing_rate.value_or(0.0f) <= 0.0f)
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warnings.emplace_back("No image indexed - no crystal lattice was determined from this dataset");
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// ---------------------------------------------- 3. GEOMETRY POST-REFINEMENT
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if (result.post_refine.has_value()) {
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const auto &pr = *result.post_refine;
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Section(os, "3. GEOMETRY POST-REFINEMENT");
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os << " The rotation two-pass fits the detector distance and beam centre from the observed spot\n"
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<< " positions, and the cell scale and rotation axis from the observed rocking angles. Each\n"
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<< " step is committed only if it improves a held-out residual.\n\n";
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Key(os, "POSTREFINE_EVENTS_USED", pr.events_used);
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Key(os, "POSTREFINE_OBS_USED", pr.obs_used);
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Key(os, "POSTREFINE_CELL_COMMITTED", pr.cell_refined ? "TRUE" : "FALSE");
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Key(os, "POSTREFINE_DETECTOR_COMMITTED", pr.detector_refined ? "TRUE" : "FALSE");
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Key(os, "POSTREFINE_DISTANCE", fmt::format("{:.3f} -> {:.3f}", pr.distance_before_mm,
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pr.distance_after_mm));
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Key(os, "POSTREFINE_BEAM_CENTRE", fmt::format("{:.2f} {:.2f} -> {:.2f} {:.2f}",
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pr.beam_x_before_px, pr.beam_y_before_px,
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pr.beam_x_after_px, pr.beam_y_after_px));
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Key(os, "GONIOMETER_ROTATION_SCALE", fmt::format("{:.5f}", pr.rotation_scale));
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Key(os, "GONIOMETER_ROTATION_SCALE_SUSPECT", pr.rotation_scale_suspect ? "TRUE" : "FALSE");
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os << "\n GONIOMETER_ROTATION_SCALE is the factor by which the stage actually turned relative to\n"
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<< " the angles stored in the file (which are the commanded ones). 1.0 = they agree. It drives\n"
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<< " the second integration pass only when SUSPECT is TRUE - both cross-validated and outside\n"
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<< " the tolerance - since a stage that is in fact well calibrated must be left alone. A\n"
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<< " manual --rotation-scale replaces it and is applied to both passes.\n";
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if (pr.rotation_scale_suspect)
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warnings.emplace_back(fmt::format(
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"The goniometer turned by a factor {:.5f} of the angles stored in the file - the "
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"stage rotation looks mis-calibrated by {:+.2f}%. The correction was applied to this "
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"run, but the fault is in the hardware and should be fixed there",
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pr.rotation_scale, 100.0 * (pr.rotation_scale - 1.0)));
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}
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// ---------------------------------------------- 4. SPACE GROUP DETERMINATION
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Section(os, "4. SPACE GROUP DETERMINATION");
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if (result.space_group_search.has_value()) {
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Key(os, "SPACE_GROUP_SEARCH", "DE_NOVO");
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os << "\n" << SearchSpaceGroupResultToText(*result.space_group_search) << "\n";
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// A centering the data could not test must not read like one they confirmed. The group may
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// still be right - the lattice metric says so - but nothing in these intensities backs it,
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// and that belongs beside the warnings rather than in a table column alone.
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const auto &search = *result.space_group_search;
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if (search.best_space_group.has_value())
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for (const auto &c : search.candidates)
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if (c.space_group.number == search.best_space_group->number && c.centering_untested)
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warnings.emplace_back(fmt::format(
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"The {} centering of {} was NOT confirmed from these data: the crystal was "
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"indexed and integrated on the primitive sub-cell, so the reflections a "
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"{}-centred lattice extinguishes are not in this merge at all. It comes "
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"from the lattice metric. The point group is confirmed from the "
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"intensities; the centering is not",
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search.best_space_group->centring_type(),
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search.best_space_group->short_name(),
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search.best_space_group->centring_type()));
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} else if (result.space_group.has_value()) {
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Key(os, "SPACE_GROUP_SEARCH", "FIXED");
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os << "\n The space group was given, not determined here.\n";
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} else {
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Key(os, "SPACE_GROUP_SEARCH", "NONE");
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os << "\n No space group was determined.\n";
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}
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// ---------------------------------------------------- 5. SCALING AND MERGING
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Section(os, "5. SCALING AND MERGING");
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if (!merged) {
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Key(os, "MERGE", "NOT_PERFORMED");
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os << "\n No scaling or merging was performed on this run, so there are no merging statistics, no\n"
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<< " error model, and no sweep-quality diagnosis below. The integrated reflections are in\n"
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<< " " << output_prefix << "_process.h5.\n";
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} else {
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const auto &o = result.merge_statistics.overall;
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Key(os, "MERGE", "PERFORMED");
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Key(os, "INCLUDE_RESOLUTION_RANGE", fmt::format("{:.3f} {:.3f}", o.d_max, o.d_min));
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Key(os, "FRIEDELS_LAW", experiment.GetScalingSettings().GetMergeFriedel() ? "TRUE" : "FALSE");
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Key(os, "UNIQUE_REFLECTIONS", o.unique_reflections);
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Key(os, "TOTAL_OBSERVATIONS", o.total_observations);
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Key(os, "COMPLETENESS", o.possible_unique_reflections > 0
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? fmt::format("{:.1f}", 100.0 * o.unique_reflections / o.possible_unique_reflections)
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: std::string("nan"));
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Key(os, "MULTIPLICITY", o.unique_reflections > 0
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? fmt::format("{:.2f}", static_cast<double>(o.total_observations) / o.unique_reflections)
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: std::string("nan"));
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Key(os, "I_OVER_SIGMA", fmt::format("{:.2f}", o.mean_i_over_sigma));
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Key(os, "R_MEAS", fmt::format("{:.4f}", o.r_meas));
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Key(os, "CC_HALF", fmt::format("{:.4f}", o.cc_half));
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Key(os, "SIGANO", fmt::format("{:.3f}", o.abs_diff_over_sigma_anomalous));
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Key(os, "WILSON_B", fmt::format("{:.2f}", result.merge_statistics.wilson_b));
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// The error model in XDS's convention, so the numbers are directly comparable with a CORRECT.LP.
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Key(os, "ERROR_MODEL_A", fmt::format("{:.4f}", result.error_model_a));
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Key(os, "ERROR_MODEL_B", fmt::format("{:.4e}", result.error_model_b));
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Key(os, "ISA", fmt::format("{:.2f}", result.error_model_isa));
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if (result.error_model_isa_asymptotic > 0.0)
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Key(os, "ISA_ASYMPTOTIC", fmt::format("{:.2f}", result.error_model_isa_asymptotic));
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Key(os, "REFERENCE_DATA_USED", result.has_reference ? "TRUE" : "FALSE");
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// The shell table straight off the statistics rather than result.merge_statistics_text: that
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// string also carries the twinning analysis and the advisories, which have sections of their own.
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os << "\n ERROR_MODEL_A / ERROR_MODEL_B are in XDS's convention, sigma^2 = a*(sigma0^2 + b*I^2),\n"
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<< " so ISA = 1/sqrt(a*b) means what CORRECT.LP's ISa means. ISA_ASYMPTOTIC, where present,\n"
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<< " is the strong-reflection tier only.\n\n"
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<< result.merge_statistics;
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}
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// --------------------------------------------------------------- 6. TWINNING
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if (merged && result.twinning.l_test_pairs > 0) {
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Section(os, "6. TWINNING");
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Key(os, "TWINNING_SUSPECTED", result.twinning.twinning_suspected ? "TRUE" : "FALSE");
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Key(os, "L_TEST_MEAN_ABS_L", fmt::format("{:.4f}", result.twinning.mean_abs_l));
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Key(os, "L_TEST_MEAN_L_SQUARED", fmt::format("{:.4f}", result.twinning.mean_l_squared));
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Key(os, "SECOND_MOMENT_I", fmt::format("{:.4f}", result.twinning.second_moment));
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Key(os, "ESTIMATED_TWIN_FRACTION", fmt::format("{:.3f}", result.twinning.estimated_twin_fraction));
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os << "\n" << TwinningAnalysisToText(result.twinning) << "\n";
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if (result.twinning.twinning_suspected)
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warnings.emplace_back(fmt::format(
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"Twinning is indicated (<|L|> = {:.3f}, <I^2>/<I>^2 = {:.3f}, estimated twin "
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"fraction {:.2f}) - refine against the merged data with care",
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result.twinning.mean_abs_l, result.twinning.second_moment,
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result.twinning.estimated_twin_fraction));
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}
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// ------------------------------------------------------- 7. RADIATION DAMAGE
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if (!result.radiation_damage_text.empty()) {
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Section(os, "7. RADIATION DAMAGE");
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// A number, or a word saying why there is none: NOT_A_TREND where the per-batch curve was measured
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// but no straight line describes it (damage is progressive, so that curve is not dose), NOT_MEASURED
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// where the monitor could not run at all.
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const double db = result.merge_statistics.radiation_damage_delta_b;
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Key(os, "RADIATION_DAMAGE_RELATIVE_B",
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std::isfinite(db) ? fmt::format("{:.2f}", db)
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: result.merge_statistics.radiation_damage_b_batch.empty() ? std::string("NOT_MEASURED")
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: std::string("NOT_A_TREND"));
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os << "\n" << result.radiation_damage_text << "\n";
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}
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// ------------------------------------------------------ 8. SWEEP QUALITY
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const auto &sq = result.merge_statistics.sweep_quality;
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Section(os, "8. SWEEP QUALITY");
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os << " Stretches of the sweep over which the crystal delivered much less than the rest of the run.\n"
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<< " REASON comes from a closed vocabulary, listed below so a consumer can tell an unknown code\n"
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<< " from a missing one. SEVERITY is the fraction of the run's typical diffracting power missing\n"
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<< " over the range (0 = as good as the run, 1 = nothing at all); SCALE and CC are the range's\n"
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<< " mean per-image scale and CC-to-merge relative to the run median; INDEXED is the fraction of\n"
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<< " the range's frames that were scaled at all. Nothing is excluded on the strength of this.\n\n";
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Key(os, "SWEEP_QUALITY_STATUS", sq.measured ? "COMPUTED" : "NOT_COMPUTED");
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Key(os, "SWEEP_QUALITY_COUNT", sq.ranges.size());
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{
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std::string codes;
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for (int r = 0; r <= static_cast<int>(SweepQualityReason::RadiationDamage); ++r)
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codes += (codes.empty() ? "" : " ")
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+ std::string(SweepQualityReasonCode(static_cast<SweepQualityReason>(r)));
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Key(os, "SWEEP_QUALITY_REASONS", codes);
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}
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if (sq.measured) {
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Key(os, "SWEEP_ROTATION", fmt::format("{:.1f}", sq.sweep_deg));
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Key(os, "FLUX_PEAK_TO_TROUGH", fmt::format("{:.2f}", sq.flux_peak_to_trough));
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Key(os, "SCALE_MODULATION_PEAK_TO_TROUGH", fmt::format("{:.2f}", sq.modulation_peak_to_trough));
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}
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os << "\n"
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<< " FIRST_IMAGE LAST_IMAGE N_IMAGES ROTATION REASON SEVERITY SCALE CC INDEXED\n"
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<< " ----------- ----------- --------- -------- -------------------- -------- ------ ------ --------\n";
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for (const auto &r : sq.ranges) {
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os << fmt::format(" {:11d} {:11d} {:9d} {:8.1f} {:<20} {:8.2f} {:6.2f} {:6.2f} {:8.2f}\n",
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r.first_image, r.last_image, r.last_image - r.first_image + 1, r.rotation_deg,
|
|
SweepQualityReasonCode(r.reason), r.severity, r.mean_relative_scale,
|
|
r.mean_relative_cc, r.indexed_fraction);
|
|
warnings.push_back(fmt::format(
|
|
"Frames {}-{} {} ({:.1f} deg, scale {:.2f} and CC {:.2f} of the run, {:.0f}% scaled)",
|
|
r.first_image, r.last_image, SweepQualityReasonText(r.reason), r.rotation_deg,
|
|
r.mean_relative_scale, r.mean_relative_cc, 100.0 * r.indexed_fraction));
|
|
}
|
|
os << " ----------- ----------- --------- -------- -------------------- -------- ------ ------ --------\n";
|
|
|
|
// ---------------------------------------------------------- 9. DIFFRACTION ANISOTROPY
|
|
const auto &an = result.merge_statistics.anisotropy;
|
|
if (merged && an.n_reflections > 0) {
|
|
Section(os, "9. DIFFRACTION ANISOTROPY");
|
|
os << " How much the fall-off depends on direction, and whether that is established above this\n"
|
|
<< " data set's own systematic error. Nothing here corrects an intensity or removes a\n"
|
|
<< " reflection: the merged data and the written files do not depend on direction at all.\n"
|
|
<< " ANISOTROPY_DELTA_B is the range of the principal components of the anisotropy tensor,\n"
|
|
<< " on the ordinary crystallographic B scale (the same scale as phenix.xtriage's B_cart and\n"
|
|
<< " ctruncate's anisotropic B), fitted on intensities with nothing dropped;\n"
|
|
<< " ANISOTROPY_SIGNIFICANCE gates ANISOTROPY_DELTA_B_LINEAR, the part of it that follows\n"
|
|
<< " exp(-1/2 s^T B s), which is not the same number. A 1 in ANISOTROPY_D_MIN_CENSORED marks\n"
|
|
<< " a direction whose limit is the edge of the measured data rather than the crystal's own.\n\n";
|
|
Key(os, "ANISOTROPY_VERDICT", AnisotropyVerdictCode(an.verdict));
|
|
Key(os, "ANISOTROPY_FREE_DIRECTIONS", an.n_free_parameters);
|
|
Key(os, "ANISOTROPY_DELTA_B", fmt::format("{:.2f}", an.delta_b));
|
|
Key(os, "ANISOTROPY_DELTA_B_LINEAR", fmt::format("{:.2f}", an.delta_b_linear));
|
|
Key(os, "ANISOTROPY_PRINCIPAL_B", fmt::format("{:.2f} {:.2f} {:.2f}",
|
|
an.eigenvalue[0] - an.eigenvalue[2],
|
|
an.eigenvalue[1] - an.eigenvalue[2], 0.0));
|
|
Key(os, "ANISOTROPY_FOLD_WEAKENING", fmt::format("{:.1f}", an.fold_weakening));
|
|
Key(os, "ANISOTROPY_D_MIN_PRINCIPAL", fmt::format("{:.2f} {:.2f} {:.2f}", an.d_min_axis[0],
|
|
an.d_min_axis[1], an.d_min_axis[2]));
|
|
Key(os, "ANISOTROPY_D_MIN_CENSORED", fmt::format("{} {} {}", an.d_min_censored[0] ? 1 : 0,
|
|
an.d_min_censored[1] ? 1 : 0,
|
|
an.d_min_censored[2] ? 1 : 0));
|
|
Key(os, "ANISOTROPY_D_MIN_SPREAD", fmt::format("{:.2f}", an.d_min_spread));
|
|
Key(os, "ANISOTROPY_SHAPE", AnisotropyShapeCode(an.shape));
|
|
Key(os, "ANISOTROPY_SHAPE_INTERCEPT", fmt::format("{:.3f}", an.shape_intercept));
|
|
Key(os, "ANISOTROPY_SHAPE_INTERCEPT_Z", fmt::format("{:.1f}", an.shape_intercept_z));
|
|
Key(os, "ANISOTROPY_SHAPE_SLOPE", fmt::format("{:.2f}", an.shape_slope));
|
|
Key(os, "ANISOTROPY_SHAPE_RESIDUAL", fmt::format("{:.1f}", an.shape_residual));
|
|
Key(os, "ANISOTROPY_N_OBSERVATIONS", an.n_observations);
|
|
Key(os, "ANISOTROPY_SIGMA_SYSTEMATIC", fmt::format("{:.3f}", an.sigma_systematic));
|
|
Key(os, "ANISOTROPY_FORBIDDEN_Z", fmt::format("{:.1f}", an.forbidden_z));
|
|
Key(os, "ANISOTROPY_FLOOR", fmt::format("{:.3f}", an.floor));
|
|
Key(os, "ANISOTROPY_SIGNIFICANCE", fmt::format("{:.2f}", an.significance));
|
|
Key(os, "ANISOTROPY_DETECTION_LIMIT", fmt::format("{:.2f}", an.detection_limit));
|
|
os << "\n" << AnisotropyToText(an) << "\n";
|
|
if (an.verdict == AnisotropyVerdict::Detected && an.d_min_spread > 0.5)
|
|
warnings.emplace_back(fmt::format(
|
|
"Diffraction is anisotropic (deltaB {:.1f} A^2; the diffraction limit runs from "
|
|
"{:.2f} to {:.2f} A depending on direction) - refinement and map interpretation "
|
|
"should allow for it; no intensity has been corrected for it here",
|
|
an.delta_b, *std::max_element(an.d_min_axis, an.d_min_axis + 3),
|
|
*std::min_element(an.d_min_axis, an.d_min_axis + 3)));
|
|
}
|
|
|
|
// ------------------------------------------------------- 10. MODEL VALIDATION
|
|
if (result.model_validation.has_value()) {
|
|
const auto &mv = *result.model_validation;
|
|
Section(os, "10. MODEL VALIDATION");
|
|
Key(os, "MODEL_FILE", mv.model_path);
|
|
if (!mv.ok) {
|
|
Key(os, "MODEL_VALIDATION", "NOT_PERFORMED");
|
|
Key(os, "MODEL_VALIDATION_REASON", mv.failure_reason);
|
|
os << "\n A model was given but could not be used, so there are no R-factors and no maps.\n"
|
|
<< " Everything else in this report is unaffected: the merge does not depend on the model.\n";
|
|
} else {
|
|
Key(os, "MODEL_SPACE_GROUP_NUMBER", mv.model_space_group_number);
|
|
Key(os, "R_WORK", fmt::format("{:.4f}", mv.r_work));
|
|
Key(os, "R_FREE", fmt::format("{:.4f}", mv.r_free));
|
|
Key(os, "R_WORK_REFLECTIONS", mv.n_work);
|
|
Key(os, "R_FREE_REFLECTIONS", mv.n_free);
|
|
Key(os, "BULK_SOLVENT_K_SOL", fmt::format("{:.3f}", mv.k_sol));
|
|
Key(os, "BULK_SOLVENT_B_SOL", fmt::format("{:.1f}", mv.b_sol));
|
|
Key(os, "SCALE_OVERALL", fmt::format("{:.4f}", mv.k_overall));
|
|
Key(os, "MEAN_ATOM_DENSITY_SIGMA", fmt::format("{:.2f}", mv.mean_atom_density_sigma));
|
|
// The anomalous scatterers the data themselves found, named by the model's atoms.
|
|
if (!mv.anomalous_sites.empty()) {
|
|
Key(os, "ANOMALOUS_BIJVOET_PAIRS", mv.anomalous_pairs);
|
|
for (size_t i = 0; i < mv.anomalous_sites.size(); i++)
|
|
// Two digits so the ten keys are the same width and the values line up.
|
|
Key(os, fmt::format("ANOMALOUS_SITE_{:02}", i + 1).c_str(),
|
|
fmt::format("{:<18} {:6.2f} sigma", mv.anomalous_sites[i].label,
|
|
mv.anomalous_sites[i].sigma));
|
|
}
|
|
// What was applied to the written reflections, so a reader can tell whether the file is
|
|
// in the indexing it was merged in or in the model's. The enantiomorph is a label only.
|
|
Key(os, "MODEL_ENANTIOMORPH_ADOPTED", mv.adopted_model_enantiomorph ? "TRUE" : "FALSE");
|
|
Key(os, "MODEL_INDEXING_OPERATOR", mv.indexing_op.triplet());
|
|
if (!mv.maps_prefix.empty())
|
|
Key(os, "MAPS_PREFIX", mv.maps_prefix);
|
|
os << "\n R-free here measures the merged intensities against an external structure, which is\n"
|
|
<< " what CC1/2 and R_meas cannot do - they only measure the data against themselves. The\n"
|
|
<< " model is not refined: it is scaled to the data with a flat bulk solvent and an overall\n"
|
|
<< " anisotropic B, so these R-factors are higher than a refined structure's and are a\n"
|
|
<< " data-quality reading, not a refinement result.\n";
|
|
if (!mv.anomalous_sites.empty())
|
|
os << "\n The anomalous sites are the highest peaks of the anomalous difference map -\n"
|
|
<< " F(+)-F(-) on the model phase turned back by 90 degrees - read at the model's own\n"
|
|
<< " atom centres, so each one is named rather than left as a coordinate. A dataset with\n"
|
|
<< " no anomalous signal still lists ten sites: it is their height, a few sigma at most,\n"
|
|
<< " that says so. The map itself is written as _anom.ccp4, where a scatterer the model\n"
|
|
<< " does not contain would show up as a peak on nothing.\n";
|
|
if (!(mv.indexing_op == gemmi::Op::identity()))
|
|
os << "\n The written reflections were reindexed into the model's frame - the operator above\n"
|
|
<< " says how - so the reflection files, the R-factors and the maps all describe one\n"
|
|
<< " indexing.\n";
|
|
if (mv.adopted_model_enantiomorph)
|
|
os << "\n The written reflections carry the model's enantiomorph as their space group. That is a\n"
|
|
<< " change of label and nothing else: the two groups of an enantiomorphic pair have the same\n"
|
|
<< " rotation operations, so no reflection moved. Reindexing by the change-of-hand operator\n"
|
|
<< " would have swapped I(+) with I(-) - flipping the anomalous differences, not correcting\n"
|
|
<< " them - on the strength of a label the space-group search reports as undetermined.\n";
|
|
if (mv.anomalous_hands_disagree)
|
|
warnings.emplace_back(fmt::format(
|
|
"The anomalous density at the model's atoms is inverted ({} reads {:.1f} sigma, deeper "
|
|
"than the highest peak) - the data and the model are in opposite hands. Either the model "
|
|
"is the wrong enantiomorph for this crystal or the data were indexed in the wrong hand; "
|
|
"the reflections have not been reindexed, which would have hidden which of the two it is",
|
|
mv.anomalous_deepest_site, mv.anomalous_deepest_sigma));
|
|
}
|
|
}
|
|
|
|
// --------------------------------------------------------------- 11. WARNINGS
|
|
if (result.cancelled)
|
|
warnings.emplace_back(fmt::format("Processing was cancelled after {} images - this report "
|
|
"describes an incomplete run", result.images_processed));
|
|
Section(os, "11. WARNINGS");
|
|
os << " Everything that needs a person's attention, one line each, marked so a script can find\n"
|
|
<< " them with a single grep for \"WARNING:\".\n\n";
|
|
Key(os, "WARNING_COUNT", warnings.size());
|
|
os << "\n";
|
|
for (const auto &w : warnings)
|
|
os << "WARNING: " << w << "\n";
|
|
if (warnings.empty())
|
|
os << " (none)\n";
|
|
|
|
os << "\n" << BANNER << "\n END OF REPORT\n" << BANNER << "\n";
|
|
return os.str();
|
|
}
|
|
|
|
void WriteResultReport(const std::string &output_prefix,
|
|
const std::string &input_file,
|
|
const DiffractionExperiment &experiment,
|
|
const ProcessResult &result,
|
|
Logger &logger,
|
|
const RunProvenance &provenance) {
|
|
if (output_prefix.empty())
|
|
return; // "compute the statistics, persist nothing"
|
|
|
|
const std::string filename = output_prefix + "_report.txt";
|
|
// The report is unconditional, so it must never be the reason a run fails: a run that produced a
|
|
// good .mtz must survive an unwritable path or a full disk. Report the failure and carry on.
|
|
try {
|
|
std::ofstream file(filename);
|
|
file.exceptions(std::ios::failbit | std::ios::badbit);
|
|
file << RenderResultReport(output_prefix, input_file, experiment, result, provenance);
|
|
} catch (const std::exception &e) {
|
|
logger.Warning("Could not write the results report {}: {}", filename, e.what());
|
|
}
|
|
}
|