leonarski_f
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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: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
87 lines
3.7 KiB
C++
87 lines
3.7 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 <vector>
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#include <mutex>
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#include "../common/SpotToSave.h"
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#include "../common/Reflection.h"
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#include "../common/DiffractionExperiment.h"
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#include "../common/PixelMask.h"
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#include "PreviewCounter.h"
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#include "../common/ColorScale.h"
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enum class PreviewImageFormat {JPEG, TIFF};
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struct PreviewImageSettings {
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std::optional<float> saturation_value = 10;
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std::optional<float> background_value = 0;
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int64_t jpeg_quality = 70;
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bool show_beam_center = true;
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bool show_spots = true;
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bool show_predictions = false;
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bool show_roi = false;
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bool show_user_mask = true;
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bool show_res_est = false;
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std::optional<float> resolution_ring;
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ColorScaleEnum scale = ColorScaleEnum::Indigo;
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PreviewImageFormat format = PreviewImageFormat::JPEG;
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};
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class PreviewImage {
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mutable std::mutex m;
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DiffractionExperiment experiment;
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std::vector<uint8_t> mask;
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std::vector<SpotToSave> spots;
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size_t xpixel = 0;
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size_t ypixel = 0;
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size_t pixel_depth_bytes = 2;
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bool pixel_is_signed = false;
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constexpr static uint8_t MaskGap = 1;
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constexpr static uint8_t MaskUsr = 2;
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constexpr static uint8_t MaskDet = 3;
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constexpr static float auto_foreground_range = 0.001f;
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template<class T>
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std::vector<rgb> GenerateRGB(const uint8_t* value,
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int64_t special_value,
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int64_t sat_value,
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const ColorScale &scale,
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const PreviewImageSettings& settings) const;
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std::vector<rgb> GenerateRGB(const PreviewImageSettings& settings, const DataMessage &msg) const;
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void AddResolutionRing(std::vector<rgb> &rgb_image, float d) const;
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void AddBeamCenter(std::vector<rgb> &rgb_image) const;
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void AddSpots(std::vector<rgb> &rgb_image, const std::vector<SpotToSave>& spots) const;
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void AddPredictions(std::vector<rgb> &rgb_image, const std::vector<Reflection>& reflections, char centering) const;
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void AddROI(std::vector<rgb> &rgb_image) const;
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// Trace a fixed-resolution arc through the geometry (a circular arc on an untilted detector,
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// a conic one on a tilted detector) by sweeping azimuth from phi_start to phi_end and joining
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// the samples. A full ring uses phi_start=0, phi_end=2*pi.
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void DrawArc(std::vector<rgb> &rgb_image, const DiffractionGeometry &geom, float d,
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float phi_start, float phi_end, const rgb &color, int halfwidth) const;
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void DrawThickLine(std::vector<rgb> &rgb_image, float x0, float y0, float x1, float y1,
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const rgb &color, int halfwidth) const;
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void DrawCircleOutline(std::vector<rgb> &rgb_image, float cx, float cy, float radius,
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int width, const rgb &color) const;
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void color_pixel(std::vector<rgb>& ret, int64_t xpixel, int64_t ypixel, const rgb &color) const;
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void spot(std::vector<rgb>& ret, int64_t xpixel, int64_t ypixel, const rgb &color) const;
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void roi(std::vector<rgb>& ret, int64_t xpixel, int64_t ypixel, int64_t roi_number) const;
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std::string GenerateImage(const PreviewImageSettings& settings, const DataMessage &msg) const;
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void ConfigurePixel(const std::vector<uint32_t> &mask, size_t pixel_begin, size_t pixel_end);
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public:
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void Configure(const DiffractionExperiment& experiment, const PixelMask& mask, size_t nthreads = 0);
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[[nodiscard]] std::string GenerateImage(const PreviewImageSettings& settings, const std::vector<uint8_t>& cbor_format);
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[[nodiscard]] static std::string GenerateTIFF(const std::vector<uint8_t>& cbor_format) ;
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};
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