The rc178 branch continued after #88 was squash-merged; this is its content fromb9ada7914(the tree #88 squashed) to094eee31a, as one change on main. The individual commits stay on the rc178 branch: - still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes - AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets - DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked - tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout - Dense per-pixel maps through the panel table (panel layout stage 1) - Panel id on spots and the panel table in the start message - Viewer and preview show a panel detector as it lies on the detector plane - Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster - Panel layout stage 2: prediction and Bragg integration through the panel table - XTC reader: frames handed up as stored, streams indexed in parallel - XFEL reader: integer frames stay integer, one gain, placement by panel - EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery" - still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed - float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count - CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them - Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table - Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane - still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good - still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file - still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition - stills fixed cost: geometry refinement and pre-scan do the same work in less wall time - stills geometry sample and trial spot finding run as many workers as the image pass - Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame - StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's - MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in) - Stills given a cell: the written cell is the mean over the frames that are merged - Stills: the radial curvature correction decided per run on the same empty apertures - StillsPartialityRefine: measure the run width only on shells with signal - Stills pre-scan: report the paired z of the radial-correction comparison - module placement: the five concurrent fits each keep every thread - still battery: score R-free against the deposited data through the same dimple protocol - still battery: the R-free target is the lower of the deposition's dimple and published values - Stills: background clip follows the radial curve; signal disk from the lattice spacing - Stills keep an overloaded observation as a lower bound instead of dropping it - Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip - battery: R-free against the deposition without refinement only, one protocol for rotation and stills - still battery: EuXFEL sets run on a 2,000-image subset for now - stills geometry refinement: fit the detector distance and the cell together - stills geometry refinement: a distance given with --detector-distance is held in the joint fit - Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count - Metal integration test: the CPU comparison runs on a rotation experiment - Stills: kept overloads go back to the drop where they are not concentrated at low resolution - stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated - battery results: XFEL still battery 20261022-1358 on rc1780cf62452c- 12 sets, cold, R_free unrefined - battery results: still summary gains the resolution of our merge and of the deposition - Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value - Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed - XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock - stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes - rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid - stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree - CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get - broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4) - frontend: Mol* viewer of the placed model and its density on the Rugnux live page - writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does - rugnux live maps: one unit cell centred on the model; the viewer opens on all of it - Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer - Mol* viewer: open with the maps drawn within 10 A of the centre of view - Mol* viewer: aaredb's structure-viewer setup, on a black stage - rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons - Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2) - ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI) - stills tilt decision: the modules stay where the run placed them - still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it - battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC - Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons - BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it - ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization - BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain - ShadowFinder: measure the modulation robustly under a wide one-sided shadow - ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation - ShadowFinder: back to the predicted polarization factor, in the plane the background shows - MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again - battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables - XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel - stills geometry trial: the hypotheses a search asks are indexed side by side - stills tilt decision: the fits start beside the pre-scan and the geometry trial - XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache - XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step - GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block - GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart - docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts - battery: doc_check.py cross-checks the manifests against the dataset pages - stills module placement: the placement fit gets half the threads, each held-out fit an eighth - still battery: the EuXFEL sets run on all their frames, as the published still runs did - battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table - macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
94 lines
4.6 KiB
C++
94 lines
4.6 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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#pragma once
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#include <chrono>
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#include <memory>
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#include <mutex>
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#include <optional>
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#include <string>
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#include <utility>
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#include <vector>
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class RugnuxStructure; // RugnuxStructure.h
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// Where the live rugnux run of the last collection is, for the broker's status route: the steps it has
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// taken with what each found ("lattice found", "space group P 21 21 21"), the step it is on and how far
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// into its images, and - once it is over - its verdict and summary as the report states them, and the
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// latency from the last image to every result written.
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//
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// Times are those of the image puller - when a message came off the socket - and every time reported is
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// in seconds since the first image arrived; until it has, since now. The START message comes earlier, by
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// start_to_first_image_s. The collection's frame rate is (images_received - 1) / last_image_s.
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enum class RugnuxLiveState { Idle, Running, Done, Failed, Cancelled, Skipped };
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struct RugnuxLiveStep {
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std::string title;
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double started_s = 0.0; // since the first image
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std::optional<double> duration_s; // set once the next step starts or the run ends
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std::vector<std::string> notes;
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};
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struct RugnuxLiveSnapshot {
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RugnuxLiveState state = RugnuxLiveState::Idle;
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std::string message; // why it failed or was skipped
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int64_t images_expected = 0;
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std::optional<double> expected_collection_s; // images_expected x the image time, as set up
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int64_t images_received = 0;
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double elapsed_s = 0.0;
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std::optional<float> step_progress; // fraction of the current pass's images
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std::vector<RugnuxLiveStep> steps;
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// The lattice probe on the first 60 degrees (JFJochReceiverRugnux::ProbeThread): an early answer
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// to "is there a crystal", seconds into the collection; the run's own answer comes later.
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std::string probe;
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std::optional<double> probe_s; // when it answered
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std::optional<double> start_to_first_image_s; // from the START message to the first image
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std::optional<double> last_image_s; // when the last image arrived; set once the collection is over
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// The analysis was cut - "deadline" (the broker's deadline_s after the last image) or "cancel" - at
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// cut_s; what it had established went out, the steps after it were left out.
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std::string cut;
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std::optional<double> cut_s;
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std::optional<double> last_image_to_written_s;
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std::string verdict; // OK | WARNINGS | UNUSABLE | FAILED
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std::string verdict_text;
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std::vector<std::pair<std::string, std::string>> summary;
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std::vector<std::string> warnings;
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// The placed model and its maps, once the run has placed one; for the viewer routes.
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std::shared_ptr<const RugnuxStructure> structure;
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};
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class RugnuxLiveStatus {
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mutable std::mutex m;
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RugnuxLiveSnapshot s;
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// Kept since the START message, shifted to the first image by Get().
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std::chrono::steady_clock::time_point start;
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std::optional<std::chrono::steady_clock::time_point> last_image;
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double Since(std::chrono::steady_clock::time_point t) const;
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double Now() const;
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void CloseStep();
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public:
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// start_received, received: when the START message and the image came off the socket (ImagePullerOutput);
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// expected_collection_s: how long the collection is set up to take, none if not known
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void Start(int64_t images_expected, std::optional<double> expected_collection_s,
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std::chrono::steady_clock::time_point start_received);
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void ImageReceived(std::chrono::steady_clock::time_point received);
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void Step(const std::string &title);
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void Note(const std::string &text);
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void Progress(uint64_t done, uint64_t total);
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void Finish(RugnuxLiveState state, const std::string &message = "");
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void Result(const std::string &verdict, const std::string &verdict_text,
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const std::vector<std::pair<std::string, std::string>> &summary,
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const std::vector<std::string> &warnings);
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void Latency(double last_image_to_written_s);
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// The collection is over: last_image_s is set, and the last image's time is returned (none if no image came).
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std::optional<std::chrono::steady_clock::time_point> LastImage();
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void Cut(const std::string &reason);
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void Probe(const std::string &text);
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void Warning(const std::string &text);
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void Structure(std::shared_ptr<const RugnuxStructure> structure);
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// Back to Idle with nothing of the last run, as before any collection.
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void Clear();
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RugnuxLiveSnapshot Get() const;
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};
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