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
124 lines
6.1 KiB
C++
124 lines
6.1 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 <cstddef>
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#include <cstdint>
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#include <optional>
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#include <utility>
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#include <vector>
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#include "ModuleShift.h"
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class DetectorGeometry;
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// One detector module: where its pixels are in the image rugnux reads, and where they really are on the
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// detector plane. The plane is the one DiffractionGeometry describes (beam centre, distance, tilt), in its
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// pixel units, so a module placed exactly as the image has it maps every pixel onto itself.
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//
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// Image pixel (x, y) of the module, x0 <= x < x0 + width, y0 <= y < y0 + height, lies on the plane at
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// (ox, oy) + (x - x0) (fx, fy) + (y - y0) (sx, sy)
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// - the NXdetector_module description (data_origin, data_size, module_offset, fast_pixel_direction,
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// slow_pixel_direction) taken in the plane. A pixel's centre is at its index, as everywhere in the image.
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struct DetectorModule {
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int64_t x0 = 0, y0 = 0, width = 0, height = 0;
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double ox = 0, oy = 0;
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double fx = 1, fy = 0;
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double sx = 0, sy = 1;
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// The module where the image has it: every pixel maps onto itself.
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static DetectorModule AsImaged(int64_t x0, int64_t y0, int64_t width, int64_t height);
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[[nodiscard]] bool ContainsImagePixel(double x, double y) const;
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[[nodiscard]] std::pair<double, double> ImageToPlane(double x, double y) const;
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[[nodiscard]] std::pair<double, double> PlaneToImage(double px, double py) const;
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// Plane position of the module's centre.
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[[nodiscard]] std::pair<double, double> PlaneCentre() const;
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// Moved by a refinement's rigid step, which is expressed on the plane (ModuleShift: turn about
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// (x0, y0) of the shift, then shift).
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void Apply(const ModuleShift &shift);
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};
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// A point in the image rugnux reads, on panel `panel` (an index into DetectorModules; -1 when the table is
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// empty and the whole image is one flat panel).
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struct PanelPoint {
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int64_t panel;
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double x, y;
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};
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// An axis-aligned box on the detector plane, x0 <= x < x1, y0 <= y < y1.
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struct PlaneBox {
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double x0, y0, x1, y1;
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};
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// The modules of one detector. Empty means the image is one flat detector: every mapping is the identity.
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// A module is a panel: one rigid box of the image with one placement. Panel ids are indices into the table.
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class DetectorModules {
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std::vector<DetectorModule> modules;
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public:
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DetectorModules() = default;
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explicit DetectorModules(std::vector<DetectorModule> modules);
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[[nodiscard]] bool empty() const;
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[[nodiscard]] size_t size() const;
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[[nodiscard]] const DetectorModule &operator[](size_t i) const;
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[[nodiscard]] const std::vector<DetectorModule> &Get() const;
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// True where some module is placed other than as imaged.
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[[nodiscard]] bool Moved() const;
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// Module of an image pixel, or -1 (a gap, or outside every module).
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[[nodiscard]] int64_t ModuleOfImagePixel(double x, double y) const;
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// Module whose placed footprint holds a plane point, or -1.
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[[nodiscard]] int64_t ModuleOfPlanePoint(double px, double py) const;
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// Image -> plane; a point on no module is left as it is.
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[[nodiscard]] std::pair<double, double> ImageToPlane(double x, double y) const;
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// Plane -> image; a point on no placed module is left as it is.
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[[nodiscard]] std::pair<double, double> PlaneToImage(double px, double py) const;
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// Image <-> plane on a known panel, no search. Panel -1 (the empty table) is the identity.
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[[nodiscard]] std::pair<double, double> ImageToPlane(int64_t panel, double x, double y) const;
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[[nodiscard]] std::pair<double, double> PlaneToImage(int64_t panel, double px, double py) const;
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// The panel whose placed footprint holds a plane point, and where that point is in the image; nullopt in
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// a gap or off every panel. Empty table: panel -1 and the point itself, wherever it is - the caller
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// bounds it by the image, as without panels.
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[[nodiscard]] std::optional<PanelPoint> PlaneToPanel(double px, double py) const;
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// Box on the plane enclosing every panel's pixels (their footprints, half a pixel beyond the edge pixel
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// centres): a quick reject before PlaneToPanel. Empty table: [0, width) x [0, height), the image
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// rectangle the bounds tests without panels use.
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[[nodiscard]] PlaneBox PlaneBounds(int64_t width, int64_t height) const;
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// Calls f(panel, index, px, py) for every image pixel on a panel - panel by panel, row by row - with
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// index = y * width + x in the image and (px, py) its centre on the plane. Pixels on no panel (gaps) are
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// not visited. Empty table: one panel -1 that is the whole image, plane == image.
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template<class F>
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void ForEachPixel(int64_t width, int64_t height, F &&f) const {
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if (modules.empty()) {
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for (int64_t y = 0; y < height; y++)
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for (int64_t x = 0; x < width; x++)
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f(int64_t(-1), static_cast<size_t>(y * width + x), static_cast<double>(x), static_cast<double>(y));
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return;
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}
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for (size_t p = 0; p < modules.size(); p++) {
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const DetectorModule &m = modules[p];
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for (int64_t y = m.y0; y < m.y0 + m.height; y++)
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for (int64_t x = m.x0; x < m.x0 + m.width; x++) {
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const auto [px, py] = m.ImageToPlane(static_cast<double>(x), static_cast<double>(y));
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f(static_cast<int64_t>(p), static_cast<size_t>(y * width + x), px, py);
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}
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}
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}
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// Each module moved by the shift whose centre is nearest its own plane centre (and within it).
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void Apply(const std::vector<ModuleShift> &shifts);
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// The modules as refinement starting points: their plane centres, no move.
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[[nodiscard]] std::vector<ModuleShift> Centres() const;
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};
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// The modules of a modular (JUNGFRAU) detector where its assembled image puts them: one box per module,
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// CONVERTED_MODULE_COLS x CONVERTED_MODULE_LINES turned the way the geometry turns it, placed as imaged.
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// Empty for a detector of one module.
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DetectorModules ModulesAsImaged(const DetectorGeometry &geom);
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