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
196 lines
7.1 KiB
C++
196 lines
7.1 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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#include "DetectorModules.h"
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#include "DetectorGeometry.h"
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#include "Definitions.h"
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#include <algorithm>
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#include <cmath>
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#include <tuple>
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DetectorModule DetectorModule::AsImaged(int64_t x0, int64_t y0, int64_t width, int64_t height) {
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DetectorModule m;
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m.x0 = x0;
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m.y0 = y0;
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m.width = width;
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m.height = height;
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m.ox = static_cast<double>(x0);
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m.oy = static_cast<double>(y0);
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return m;
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}
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bool DetectorModule::ContainsImagePixel(double x, double y) const {
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// A pixel's centre is at its index, so the module covers [x0 - 0.5, x0 + width - 0.5).
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return x >= static_cast<double>(x0) - 0.5 && x < static_cast<double>(x0 + width) - 0.5
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&& y >= static_cast<double>(y0) - 0.5 && y < static_cast<double>(y0 + height) - 0.5;
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}
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std::pair<double, double> DetectorModule::ImageToPlane(double x, double y) const {
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const double u = x - static_cast<double>(x0), v = y - static_cast<double>(y0);
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return {ox + u * fx + v * sx, oy + u * fy + v * sy};
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}
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std::pair<double, double> DetectorModule::PlaneToImage(double px, double py) const {
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// Inverse of the 2x2 [f s]
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const double det = fx * sy - sx * fy;
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const double dx = px - ox, dy = py - oy;
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const double u = (sy * dx - sx * dy) / det;
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const double v = (-fy * dx + fx * dy) / det;
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return {static_cast<double>(x0) + u, static_cast<double>(y0) + v};
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}
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std::pair<double, double> DetectorModule::PlaneCentre() const {
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return ImageToPlane(static_cast<double>(x0) + 0.5 * static_cast<double>(width - 1),
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static_cast<double>(y0) + 0.5 * static_cast<double>(height - 1));
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}
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void DetectorModule::Apply(const ModuleShift &shift) {
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const double c = std::cos(shift.rot_rad), s = std::sin(shift.rot_rad);
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const double ux = ox - shift.x0, uy = oy - shift.y0;
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ox = shift.x0 + c * ux - s * uy + shift.dx;
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oy = shift.y0 + s * ux + c * uy + shift.dy;
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const double nfx = c * fx - s * fy, nfy = s * fx + c * fy;
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const double nsx = c * sx - s * sy, nsy = s * sx + c * sy;
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fx = nfx; fy = nfy;
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sx = nsx; sy = nsy;
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}
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DetectorModules::DetectorModules(std::vector<DetectorModule> in) : modules(std::move(in)) {}
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bool DetectorModules::empty() const {
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return modules.empty();
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}
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size_t DetectorModules::size() const {
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return modules.size();
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}
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const DetectorModule &DetectorModules::operator[](size_t i) const {
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return modules.at(i);
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}
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const std::vector<DetectorModule> &DetectorModules::Get() const {
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return modules;
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}
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bool DetectorModules::Moved() const {
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for (const auto &m: modules)
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if (m.ox != static_cast<double>(m.x0) || m.oy != static_cast<double>(m.y0)
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|| m.fx != 1.0 || m.fy != 0.0 || m.sx != 0.0 || m.sy != 1.0)
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return true;
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return false;
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}
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int64_t DetectorModules::ModuleOfImagePixel(double x, double y) const {
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for (size_t i = 0; i < modules.size(); i++)
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if (modules[i].ContainsImagePixel(x, y))
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return static_cast<int64_t>(i);
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return -1;
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}
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int64_t DetectorModules::ModuleOfPlanePoint(double px, double py) const {
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for (size_t i = 0; i < modules.size(); i++) {
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const auto [x, y] = modules[i].PlaneToImage(px, py);
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if (modules[i].ContainsImagePixel(x, y))
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return static_cast<int64_t>(i);
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}
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return -1;
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}
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std::pair<double, double> DetectorModules::ImageToPlane(double x, double y) const {
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const int64_t m = ModuleOfImagePixel(x, y);
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if (m < 0)
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return {x, y};
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return modules[m].ImageToPlane(x, y);
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}
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std::pair<double, double> DetectorModules::PlaneToImage(double px, double py) const {
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const int64_t m = ModuleOfPlanePoint(px, py);
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if (m < 0)
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return {px, py};
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return modules[m].PlaneToImage(px, py);
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}
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std::pair<double, double> DetectorModules::ImageToPlane(int64_t panel, double x, double y) const {
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if (panel < 0)
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return {x, y};
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return modules.at(panel).ImageToPlane(x, y);
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}
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std::pair<double, double> DetectorModules::PlaneToImage(int64_t panel, double px, double py) const {
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if (panel < 0)
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return {px, py};
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return modules.at(panel).PlaneToImage(px, py);
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}
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std::optional<PanelPoint> DetectorModules::PlaneToPanel(double px, double py) const {
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if (modules.empty())
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return PanelPoint{-1, px, py};
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for (size_t i = 0; i < modules.size(); i++) {
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const auto [x, y] = modules[i].PlaneToImage(px, py);
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if (modules[i].ContainsImagePixel(x, y))
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return PanelPoint{static_cast<int64_t>(i), x, y};
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}
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return std::nullopt;
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}
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PlaneBox DetectorModules::PlaneBounds(int64_t width, int64_t height) const {
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if (modules.empty())
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return {0.0, 0.0, static_cast<double>(width), static_cast<double>(height)};
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PlaneBox box{INFINITY, INFINITY, -INFINITY, -INFINITY};
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for (const auto &m: modules) {
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const double xa = static_cast<double>(m.x0) - 0.5, xb = static_cast<double>(m.x0 + m.width) - 0.5;
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const double ya = static_cast<double>(m.y0) - 0.5, yb = static_cast<double>(m.y0 + m.height) - 0.5;
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for (const auto &[x, y]: {std::pair{xa, ya}, std::pair{xb, ya}, std::pair{xa, yb}, std::pair{xb, yb}}) {
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const auto [px, py] = m.ImageToPlane(x, y);
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box.x0 = std::min(box.x0, px);
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box.y0 = std::min(box.y0, py);
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box.x1 = std::max(box.x1, px);
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box.y1 = std::max(box.y1, py);
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}
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}
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return box;
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}
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void DetectorModules::Apply(const std::vector<ModuleShift> &shifts) {
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for (auto &m: modules) {
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const auto [cx, cy] = m.PlaneCentre();
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const double reach = 0.5 * static_cast<double>(std::min(m.width, m.height));
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const ModuleShift *best = nullptr;
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for (const auto &s: shifts)
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if (std::hypot(s.x0 - cx, s.y0 - cy) < reach
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&& (!best || std::hypot(s.x0 - cx, s.y0 - cy) < std::hypot(best->x0 - cx, best->y0 - cy)))
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best = &s;
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if (best)
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m.Apply(*best);
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}
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}
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std::vector<ModuleShift> DetectorModules::Centres() const {
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std::vector<ModuleShift> out;
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for (const auto &m: modules) {
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ModuleShift s;
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std::tie(s.x0, s.y0) = m.PlaneCentre();
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out.push_back(s);
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}
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return out;
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}
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DetectorModules ModulesAsImaged(const DetectorGeometry &geom) {
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if (geom.GetModulesNum() < 2)
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return {};
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std::vector<DetectorModule> out;
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for (int64_t m = 0; m < geom.GetModulesNum(); m++) {
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const Coord f = geom.GetFastDirection(m), s = geom.GetSlowDirection(m);
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const double cols = CONVERTED_MODULE_COLS - 1, lines = CONVERTED_MODULE_LINES - 1;
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const double xa = static_cast<double>(geom.GetX0(m)), ya = static_cast<double>(geom.GetY0(m));
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const double xb = xa + cols * f.x + lines * s.x, yb = ya + cols * f.y + lines * s.y;
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const auto x0 = static_cast<int64_t>(std::lround(std::min(xa, xb)));
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const auto y0 = static_cast<int64_t>(std::lround(std::min(ya, yb)));
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out.push_back(DetectorModule::AsImaged(x0, y0, std::lround(std::abs(xb - xa)) + 1,
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std::lround(std::abs(yb - ya)) + 1));
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}
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return DetectorModules(out);
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}
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