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Jungfraujoch/common/DetectorModules.cpp
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leonarski_fandClaude Opus 5.5 0a515bb086 rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG
The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, 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 rc178 0cf62452c - 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
2026-10-23 17:56:42 +02:00

196 lines
7.1 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "DetectorModules.h"
#include "DetectorGeometry.h"
#include "Definitions.h"
#include <algorithm>
#include <cmath>
#include <tuple>
DetectorModule DetectorModule::AsImaged(int64_t x0, int64_t y0, int64_t width, int64_t height) {
DetectorModule m;
m.x0 = x0;
m.y0 = y0;
m.width = width;
m.height = height;
m.ox = static_cast<double>(x0);
m.oy = static_cast<double>(y0);
return m;
}
bool DetectorModule::ContainsImagePixel(double x, double y) const {
// A pixel's centre is at its index, so the module covers [x0 - 0.5, x0 + width - 0.5).
return x >= static_cast<double>(x0) - 0.5 && x < static_cast<double>(x0 + width) - 0.5
&& y >= static_cast<double>(y0) - 0.5 && y < static_cast<double>(y0 + height) - 0.5;
}
std::pair<double, double> DetectorModule::ImageToPlane(double x, double y) const {
const double u = x - static_cast<double>(x0), v = y - static_cast<double>(y0);
return {ox + u * fx + v * sx, oy + u * fy + v * sy};
}
std::pair<double, double> DetectorModule::PlaneToImage(double px, double py) const {
// Inverse of the 2x2 [f s]
const double det = fx * sy - sx * fy;
const double dx = px - ox, dy = py - oy;
const double u = (sy * dx - sx * dy) / det;
const double v = (-fy * dx + fx * dy) / det;
return {static_cast<double>(x0) + u, static_cast<double>(y0) + v};
}
std::pair<double, double> DetectorModule::PlaneCentre() const {
return ImageToPlane(static_cast<double>(x0) + 0.5 * static_cast<double>(width - 1),
static_cast<double>(y0) + 0.5 * static_cast<double>(height - 1));
}
void DetectorModule::Apply(const ModuleShift &shift) {
const double c = std::cos(shift.rot_rad), s = std::sin(shift.rot_rad);
const double ux = ox - shift.x0, uy = oy - shift.y0;
ox = shift.x0 + c * ux - s * uy + shift.dx;
oy = shift.y0 + s * ux + c * uy + shift.dy;
const double nfx = c * fx - s * fy, nfy = s * fx + c * fy;
const double nsx = c * sx - s * sy, nsy = s * sx + c * sy;
fx = nfx; fy = nfy;
sx = nsx; sy = nsy;
}
DetectorModules::DetectorModules(std::vector<DetectorModule> in) : modules(std::move(in)) {}
bool DetectorModules::empty() const {
return modules.empty();
}
size_t DetectorModules::size() const {
return modules.size();
}
const DetectorModule &DetectorModules::operator[](size_t i) const {
return modules.at(i);
}
const std::vector<DetectorModule> &DetectorModules::Get() const {
return modules;
}
bool DetectorModules::Moved() const {
for (const auto &m: modules)
if (m.ox != static_cast<double>(m.x0) || m.oy != static_cast<double>(m.y0)
|| m.fx != 1.0 || m.fy != 0.0 || m.sx != 0.0 || m.sy != 1.0)
return true;
return false;
}
int64_t DetectorModules::ModuleOfImagePixel(double x, double y) const {
for (size_t i = 0; i < modules.size(); i++)
if (modules[i].ContainsImagePixel(x, y))
return static_cast<int64_t>(i);
return -1;
}
int64_t DetectorModules::ModuleOfPlanePoint(double px, double py) const {
for (size_t i = 0; i < modules.size(); i++) {
const auto [x, y] = modules[i].PlaneToImage(px, py);
if (modules[i].ContainsImagePixel(x, y))
return static_cast<int64_t>(i);
}
return -1;
}
std::pair<double, double> DetectorModules::ImageToPlane(double x, double y) const {
const int64_t m = ModuleOfImagePixel(x, y);
if (m < 0)
return {x, y};
return modules[m].ImageToPlane(x, y);
}
std::pair<double, double> DetectorModules::PlaneToImage(double px, double py) const {
const int64_t m = ModuleOfPlanePoint(px, py);
if (m < 0)
return {px, py};
return modules[m].PlaneToImage(px, py);
}
std::pair<double, double> DetectorModules::ImageToPlane(int64_t panel, double x, double y) const {
if (panel < 0)
return {x, y};
return modules.at(panel).ImageToPlane(x, y);
}
std::pair<double, double> DetectorModules::PlaneToImage(int64_t panel, double px, double py) const {
if (panel < 0)
return {px, py};
return modules.at(panel).PlaneToImage(px, py);
}
std::optional<PanelPoint> DetectorModules::PlaneToPanel(double px, double py) const {
if (modules.empty())
return PanelPoint{-1, px, py};
for (size_t i = 0; i < modules.size(); i++) {
const auto [x, y] = modules[i].PlaneToImage(px, py);
if (modules[i].ContainsImagePixel(x, y))
return PanelPoint{static_cast<int64_t>(i), x, y};
}
return std::nullopt;
}
PlaneBox DetectorModules::PlaneBounds(int64_t width, int64_t height) const {
if (modules.empty())
return {0.0, 0.0, static_cast<double>(width), static_cast<double>(height)};
PlaneBox box{INFINITY, INFINITY, -INFINITY, -INFINITY};
for (const auto &m: modules) {
const double xa = static_cast<double>(m.x0) - 0.5, xb = static_cast<double>(m.x0 + m.width) - 0.5;
const double ya = static_cast<double>(m.y0) - 0.5, yb = static_cast<double>(m.y0 + m.height) - 0.5;
for (const auto &[x, y]: {std::pair{xa, ya}, std::pair{xb, ya}, std::pair{xa, yb}, std::pair{xb, yb}}) {
const auto [px, py] = m.ImageToPlane(x, y);
box.x0 = std::min(box.x0, px);
box.y0 = std::min(box.y0, py);
box.x1 = std::max(box.x1, px);
box.y1 = std::max(box.y1, py);
}
}
return box;
}
void DetectorModules::Apply(const std::vector<ModuleShift> &shifts) {
for (auto &m: modules) {
const auto [cx, cy] = m.PlaneCentre();
const double reach = 0.5 * static_cast<double>(std::min(m.width, m.height));
const ModuleShift *best = nullptr;
for (const auto &s: shifts)
if (std::hypot(s.x0 - cx, s.y0 - cy) < reach
&& (!best || std::hypot(s.x0 - cx, s.y0 - cy) < std::hypot(best->x0 - cx, best->y0 - cy)))
best = &s;
if (best)
m.Apply(*best);
}
}
std::vector<ModuleShift> DetectorModules::Centres() const {
std::vector<ModuleShift> out;
for (const auto &m: modules) {
ModuleShift s;
std::tie(s.x0, s.y0) = m.PlaneCentre();
out.push_back(s);
}
return out;
}
DetectorModules ModulesAsImaged(const DetectorGeometry &geom) {
if (geom.GetModulesNum() < 2)
return {};
std::vector<DetectorModule> out;
for (int64_t m = 0; m < geom.GetModulesNum(); m++) {
const Coord f = geom.GetFastDirection(m), s = geom.GetSlowDirection(m);
const double cols = CONVERTED_MODULE_COLS - 1, lines = CONVERTED_MODULE_LINES - 1;
const double xa = static_cast<double>(geom.GetX0(m)), ya = static_cast<double>(geom.GetY0(m));
const double xb = xa + cols * f.x + lines * s.x, yb = ya + cols * f.y + lines * s.y;
const auto x0 = static_cast<int64_t>(std::lround(std::min(xa, xb)));
const auto y0 = static_cast<int64_t>(std::lround(std::min(ya, yb)));
out.push_back(DetectorModule::AsImaged(x0, y0, std::lround(std::abs(xb - xa)) + 1,
std::lround(std::abs(yb - ya)) + 1));
}
return DetectorModules(out);
}