leonarski_f
538f3504d3
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
44 lines
1.7 KiB
C++
44 lines
1.7 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include "../../common/DiffractionExperiment.h"
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#include "../../common/DiffractionSpot.h"
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#include "../../fpga/pcie_driver/jfjoch_fpga.h" // DeviceOutput
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#include "SpotFindingSettings.h"
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struct strong_pixel {
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uint16_t col;
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uint16_t line;
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int32_t counts;
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};
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class StrongPixelSet {
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std::vector<strong_pixel> pixels;
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std::vector<uint32_t> L;
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static const constexpr size_t max_strong_pixel_per_module = 4000;
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static const constexpr uint32_t xpixel = RAW_MODULE_COLS;
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static const constexpr uint32_t ypixel = RAW_MODULE_LINES;
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uint32_t strong_pixel_count;
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uint32_t find_root(uint32_t e);
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uint32_t make_union(uint32_t e1, uint32_t e2);
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std::vector<DiffractionSpot> sparseccl();
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public:
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void ReadFPGAOutput(const DiffractionExperiment& experiment,
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const DeviceOutput& output);
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StrongPixelSet();
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void AddStrongPixel(uint16_t col, uint16_t line, int32_t photons = 1);
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void FindSpots(const DiffractionExperiment &experiment, const SpotFindingSettings &settings, std::vector<DiffractionSpot> &spots,
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uint16_t module_number);
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// Every connected component of at most max-pix pixels. min-pix is deliberately NOT applied: it is
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// the only spot setting that changes between the passes of the per-image min-pix search, so one
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// connected-component search serves all of them (see ImageSpotFinder::ExtractComponents).
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void FindComponentsImage(const SpotFindingSettings &settings, std::vector<DiffractionSpot> &spots);
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uint32_t GetStrongPixelCount() const;
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};
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