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
69 lines
3.7 KiB
C++
69 lines
3.7 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 <algorithm>
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#include <cmath>
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#include <cstdint>
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#include <vector>
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#include "DetectorModules.h"
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// The detector plane as a picture: raster pixel (i, j) is the plane point (x0 + i, y0 + j). For the
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// algorithms that need the detector as it really is - a beam-stop shadow and the gaps it crosses, the point
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// symmetry about the beam, a picture of the detector - and not as the panels are stored.
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struct PlaneRaster {
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int64_t x0 = 0, y0 = 0, width = 0, height = 0;
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};
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// The raster holding every panel. It starts at the plane origin, so plane and raster coordinates agree,
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// unless a panel lies left of or above it. Empty table: the image itself.
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PlaneRaster PlaneRasterOf(const DetectorModules &modules, int64_t width, int64_t height);
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// The image (width x height) as the plane raster: each raster pixel takes the image pixel nearest its centre
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// on the panel it falls on, and `gap` where it falls on none. Empty table, with the image's own raster: a copy.
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template<class T>
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std::vector<T> AssembleToPlane(const DetectorModules &modules, const std::vector<T> &image,
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int64_t width, int64_t height, const PlaneRaster &raster, T gap) {
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std::vector<T> out(static_cast<size_t>(raster.width * raster.height), gap);
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const auto put = [&](const DetectorModule &m, int64_t i0, int64_t i1, int64_t j0, int64_t j1) {
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for (int64_t j = std::max<int64_t>(j0, 0); j < std::min(j1, raster.height); j++)
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for (int64_t i = std::max<int64_t>(i0, 0); i < std::min(i1, raster.width); i++) {
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const auto [x, y] = m.PlaneToImage(static_cast<double>(raster.x0 + i),
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static_cast<double>(raster.y0 + j));
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if (m.ContainsImagePixel(x, y))
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out[j * raster.width + i] = image[static_cast<size_t>(std::floor(y + 0.5)) * width
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+ static_cast<size_t>(std::floor(x + 0.5))];
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}
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};
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if (modules.empty()) {
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put(DetectorModule::AsImaged(0, 0, width, height), -raster.x0, width - raster.x0, -raster.y0,
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height - raster.y0);
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return out;
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}
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// Panel by panel, over the raster pixels of its footprint's box. Panels do not overlap.
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for (const auto &m: modules.Get()) {
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const PlaneBox box = DetectorModules({m}).PlaneBounds(width, height);
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put(m, static_cast<int64_t>(std::floor(box.x0)) - raster.x0, static_cast<int64_t>(std::ceil(box.x1)) - raster.x0,
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static_cast<int64_t>(std::floor(box.y0)) - raster.y0, static_cast<int64_t>(std::ceil(box.y1)) - raster.y0);
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}
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return out;
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}
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// The reverse, for a result computed on the raster: each image pixel on a panel takes the raster pixel
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// nearest its centre on the plane, `outside` where that is off the raster; a pixel on no panel (a gap)
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// is `outside` too. Empty table, with the image's own raster: a copy.
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template<class T>
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std::vector<T> GatherFromPlane(const DetectorModules &modules, const std::vector<T> &plane,
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const PlaneRaster &raster, int64_t width, int64_t height, T outside) {
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std::vector<T> out(static_cast<size_t>(width * height), outside);
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modules.ForEachPixel(width, height, [&](int64_t, size_t index, double px, double py) {
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const auto i = static_cast<int64_t>(std::floor(px + 0.5)) - raster.x0;
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const auto j = static_cast<int64_t>(std::floor(py + 0.5)) - raster.y0;
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if (i >= 0 && i < raster.width && j >= 0 && j < raster.height)
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out[index] = plane[j * raster.width + i];
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});
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return out;
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}
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