Files
Jungfraujoch/common/DetectorModules.h
T
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

124 lines
6.1 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <cstddef>
#include <cstdint>
#include <optional>
#include <utility>
#include <vector>
#include "ModuleShift.h"
class DetectorGeometry;
// One detector module: where its pixels are in the image rugnux reads, and where they really are on the
// detector plane. The plane is the one DiffractionGeometry describes (beam centre, distance, tilt), in its
// pixel units, so a module placed exactly as the image has it maps every pixel onto itself.
//
// Image pixel (x, y) of the module, x0 <= x < x0 + width, y0 <= y < y0 + height, lies on the plane at
// (ox, oy) + (x - x0) (fx, fy) + (y - y0) (sx, sy)
// - the NXdetector_module description (data_origin, data_size, module_offset, fast_pixel_direction,
// slow_pixel_direction) taken in the plane. A pixel's centre is at its index, as everywhere in the image.
struct DetectorModule {
int64_t x0 = 0, y0 = 0, width = 0, height = 0;
double ox = 0, oy = 0;
double fx = 1, fy = 0;
double sx = 0, sy = 1;
// The module where the image has it: every pixel maps onto itself.
static DetectorModule AsImaged(int64_t x0, int64_t y0, int64_t width, int64_t height);
[[nodiscard]] bool ContainsImagePixel(double x, double y) const;
[[nodiscard]] std::pair<double, double> ImageToPlane(double x, double y) const;
[[nodiscard]] std::pair<double, double> PlaneToImage(double px, double py) const;
// Plane position of the module's centre.
[[nodiscard]] std::pair<double, double> PlaneCentre() const;
// Moved by a refinement's rigid step, which is expressed on the plane (ModuleShift: turn about
// (x0, y0) of the shift, then shift).
void Apply(const ModuleShift &shift);
};
// A point in the image rugnux reads, on panel `panel` (an index into DetectorModules; -1 when the table is
// empty and the whole image is one flat panel).
struct PanelPoint {
int64_t panel;
double x, y;
};
// An axis-aligned box on the detector plane, x0 <= x < x1, y0 <= y < y1.
struct PlaneBox {
double x0, y0, x1, y1;
};
// The modules of one detector. Empty means the image is one flat detector: every mapping is the identity.
// A module is a panel: one rigid box of the image with one placement. Panel ids are indices into the table.
class DetectorModules {
std::vector<DetectorModule> modules;
public:
DetectorModules() = default;
explicit DetectorModules(std::vector<DetectorModule> modules);
[[nodiscard]] bool empty() const;
[[nodiscard]] size_t size() const;
[[nodiscard]] const DetectorModule &operator[](size_t i) const;
[[nodiscard]] const std::vector<DetectorModule> &Get() const;
// True where some module is placed other than as imaged.
[[nodiscard]] bool Moved() const;
// Module of an image pixel, or -1 (a gap, or outside every module).
[[nodiscard]] int64_t ModuleOfImagePixel(double x, double y) const;
// Module whose placed footprint holds a plane point, or -1.
[[nodiscard]] int64_t ModuleOfPlanePoint(double px, double py) const;
// Image -> plane; a point on no module is left as it is.
[[nodiscard]] std::pair<double, double> ImageToPlane(double x, double y) const;
// Plane -> image; a point on no placed module is left as it is.
[[nodiscard]] std::pair<double, double> PlaneToImage(double px, double py) const;
// Image <-> plane on a known panel, no search. Panel -1 (the empty table) is the identity.
[[nodiscard]] std::pair<double, double> ImageToPlane(int64_t panel, double x, double y) const;
[[nodiscard]] std::pair<double, double> PlaneToImage(int64_t panel, double px, double py) const;
// The panel whose placed footprint holds a plane point, and where that point is in the image; nullopt in
// a gap or off every panel. Empty table: panel -1 and the point itself, wherever it is - the caller
// bounds it by the image, as without panels.
[[nodiscard]] std::optional<PanelPoint> PlaneToPanel(double px, double py) const;
// Box on the plane enclosing every panel's pixels (their footprints, half a pixel beyond the edge pixel
// centres): a quick reject before PlaneToPanel. Empty table: [0, width) x [0, height), the image
// rectangle the bounds tests without panels use.
[[nodiscard]] PlaneBox PlaneBounds(int64_t width, int64_t height) const;
// Calls f(panel, index, px, py) for every image pixel on a panel - panel by panel, row by row - with
// index = y * width + x in the image and (px, py) its centre on the plane. Pixels on no panel (gaps) are
// not visited. Empty table: one panel -1 that is the whole image, plane == image.
template<class F>
void ForEachPixel(int64_t width, int64_t height, F &&f) const {
if (modules.empty()) {
for (int64_t y = 0; y < height; y++)
for (int64_t x = 0; x < width; x++)
f(int64_t(-1), static_cast<size_t>(y * width + x), static_cast<double>(x), static_cast<double>(y));
return;
}
for (size_t p = 0; p < modules.size(); p++) {
const DetectorModule &m = modules[p];
for (int64_t y = m.y0; y < m.y0 + m.height; y++)
for (int64_t x = m.x0; x < m.x0 + m.width; x++) {
const auto [px, py] = m.ImageToPlane(static_cast<double>(x), static_cast<double>(y));
f(static_cast<int64_t>(p), static_cast<size_t>(y * width + x), px, py);
}
}
}
// Each module moved by the shift whose centre is nearest its own plane centre (and within it).
void Apply(const std::vector<ModuleShift> &shifts);
// The modules as refinement starting points: their plane centres, no move.
[[nodiscard]] std::vector<ModuleShift> Centres() const;
};
// The modules of a modular (JUNGFRAU) detector where its assembled image puts them: one box per module,
// CONVERTED_MODULE_COLS x CONVERTED_MODULE_LINES turned the way the geometry turns it, placed as imaged.
// Empty for a detector of one module.
DetectorModules ModulesAsImaged(const DetectorGeometry &geom);