leonarski_fandClaude Opus 5.5
59d92a7238
Two whole-dataset sorts sat on the main thread at the end of a rotation run: WilsonOutliers orders every full by resolution, and the unmerged MTZ is put in H K L M/ISYM BATCH order by Mtz::sort(5) - together about 2 s of one thread on a 1.4 M-observation set. ParallelSort (common/ParallelFor.h) sorts one piece per worker and merges them pairwise. It is only for comparators that are a strict total order, where the sorted sequence is unique and the result is the serial sort's bit for bit: WilsonOutliers already breaks ties on the index, and the unmerged writer now sorts the rows itself on the five key columns and then the row number - the order Mtz::sort's stable sort gives - and sets sort_order as it did. An empty table still fails the way Mtz::sort does. md5-identical p.hkl, p.mtz and p_unmerged.mtz; 44.4 -> 43.6 s on a 16M set. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
78 lines
4.1 KiB
C++
78 lines
4.1 KiB
C++
// SPDX-FileCopyrightText: 2025 Paul Scherrer Institute
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <string>
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#include <vector>
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#include "../common/Reflection.h"
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#include "../common/UnitCell.h"
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#include "../common/DiffractionExperiment.h"
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#include "IntegrationOutcome.h"
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struct MergeStatistics;
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struct TwinningAnalysisResult;
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// The error model as it is reported, already formatted. `isa` is the whole-range 1/sqrt(a*b), the
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// same quantity XDS's ISa denotes, so a file written here is directly comparable with a CORRECT.LP;
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// `isa_asymptotic` is the strong-reflection tier, which only the rotation path has. `a` and `b` are
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// in XDS's convention, sigma^2 = a*(sigma0^2 + b*I^2). Empty strings are written as unknown.
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struct ErrorModelReport {
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std::string isa;
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std::string isa_asymptotic;
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std::string a;
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std::string b;
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};
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// nthreads: workers for the per-reflection row formatting, which is the bulk of the file.
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void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
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const UnitCell &unitCell,
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const DiffractionExperiment &experiment,
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const MergeStatistics &statistics,
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const ErrorModelReport &error_model,
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const TwinningAnalysisResult &twinning,
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const std::string &filename,
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size_t nthreads);
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void WriteMtzReflections(const std::vector<MergedReflection> &reflections,
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const UnitCell &unitCell,
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const DiffractionExperiment &experiment,
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const std::string &filename);
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// SHELX HKLF-4 text file (h k l I sigma(I), Bijvoet mates separate) for SHELXC / ANODE.
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// nthreads: workers for the per-reflection row formatting, as for the mmCIF.
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void WriteShelxHklReflections(const std::vector<MergedReflection> &reflections,
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const DiffractionExperiment &experiment,
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const std::string &filename,
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size_t nthreads);
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// Unmerged observations in the column and batch-header layout POINTLESS writes: aimless, pointless,
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// careless and iotbx.merging_statistics all read that layout. H K L are the ASU indices and M/ISYM
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// recovers the index the reflection was measured at (which is what careless needs to see the crystal
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// frame) and says whether the observation is a partial.
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// sum_partials: add the partials of each rocking event into one full, written at the batch of the
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// event's centroid with the summed rocking-curve fraction in FRACTIONCALC - the plain sum every
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// rotation program writes, over the events the combine would assemble (--min-partiality). False
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// writes one row per integrated box instead, flagged as partials for the reading program to sum.
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// Stills have no rocking events and are unaffected either way.
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// The intensities carry the deterministic per-reflection corrections and nothing else - Lorentz
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// and polarization in LP, the sensor's angle-dependent efficiency in QE, and the attenuation of the
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// flight-path medium in FLIGHT - so raw counts are I / LP * QE * FLIGHT. The partiality and the
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// per-image scale are left for the reading program to fit, since every program this file is for
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// fits a scale model of its own.
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void WriteUnmergedMtzReflections(const std::vector<IntegrationOutcome> &outcomes,
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const UnitCell &unitCell,
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const DiffractionExperiment &experiment,
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bool sum_partials,
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const std::string &filename,
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size_t nthreads = 1);
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void WriteReflections(const std::vector<MergedReflection> &reflections,
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const UnitCell &unitCell,
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const DiffractionExperiment &experiment,
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const MergeStatistics &statistics,
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const ErrorModelReport &error_model,
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const TwinningAnalysisResult &twinning,
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const std::string &filename,
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size_t nthreads); |