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>
88 lines
3.1 KiB
C++
88 lines
3.1 KiB
C++
// SPDX-FileCopyrightText: 2025 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 <vector>
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#include <unordered_set>
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#include <map>
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#include <mutex>
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#include <optional>
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#include "../common/TopPixels.h"
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#include "JFJochReaderDataset.h"
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#include "../common/CrystalLattice.h"
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#include "../common/Histogram.h"
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// Markers stored in place of an intensity. They occupy the bottom of the int32 range and
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// INT32_MAX at the top, so anything in between is a real count. Add a marker at the BOTTOM and move
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// MIN_REAL_PXL_VALUE with it - several places classify a pixel by range rather than by equality,
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// and they all test against MIN_REAL_PXL_VALUE.
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constexpr static int32_t ERROR_PXL_VALUE = INT32_MIN;
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constexpr static int32_t GAP_PXL_VALUE = INT32_MIN + 1;
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constexpr static int32_t BEAM_STOP_PXL_VALUE = INT32_MIN + 2;
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constexpr static int32_t MIN_REAL_PXL_VALUE = INT32_MIN + 3;
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constexpr static int32_t SATURATED_PXL_VALUE = INT32_MAX;
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struct JFJochReaderRawImage {
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std::vector<uint8_t> image_buffer;
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CompressedImage image;
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};
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class JFJochReaderImage {
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std::shared_ptr<const JFJochReaderDataset> dataset;
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std::vector<int32_t> image; // Image in the reader must be 32-bit signed, uncompressed
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DataMessage message;
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std::unordered_set<int64_t> saturated_pixel;
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std::unordered_set<int64_t> error_pixel;
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std::vector<std::pair<int32_t, int32_t>> valid_pixel;
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// Fast stats without storing/sorting all valid pixels
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int32_t valid_min = 0;
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int32_t valid_max = 0;
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size_t valid_count = 0;
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bool has_valid = false;
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// For overlay: track top pixels with a tiny O(K) structure; export to vector for UI
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TopPixels top_pixels_acc{20};
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std::vector<std::pair<int32_t, int32_t>> top_pixels;
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// This histogram operates in square root of count from 0 to 10^20
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Histogram count_histogram{100000};
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constexpr static float auto_foreground_range = 99.0f;
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int32_t auto_foreground;
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void CalcAutoContrast();
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template <class T>
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void ProcessInputImage(const void* image, size_t npixel, int64_t sat_value, int64_t special_value);
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void ProcessInputImage(const CompressedImage& image);
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public:
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JFJochReaderImage(const DataMessage &msg, const std::shared_ptr<const JFJochReaderDataset> &dataset);
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JFJochReaderImage(const JFJochReaderImage &other);
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const DataMessage &ImageData() const;
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DataMessage &ImageData();
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const std::vector<int32_t> &Image() const;
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const std::unordered_set<int64_t> &SaturatedPixels() const;
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const std::unordered_set<int64_t> &ErrorPixels() const;
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const JFJochReaderDataset &Dataset() const;
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std::optional<std::pair<int32_t, int32_t>> ValidMinMax() const;
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const std::vector<std::pair<int32_t, int32_t>> &GetTopPixels() const;
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void AddImage(const JFJochReaderImage& other);
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std::vector<float> GetAzInt1D() const;
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std::vector<float> GetAzInt1D_BinToQ() const;
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std::shared_ptr<JFJochReaderDataset> CreateMutableDataset();
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int32_t GetAutoContrastValue() const;
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std::vector<float> GetHistogram() const;
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};
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