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Jungfraujoch/image_analysis/geom_refinement/BackgroundBand.h
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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

122 lines
5.9 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
// Where one pixel falls in the background beam-centre fit (FindBeamCenterFromBackground): which
// radial-bin x sector cell of the fitted band it lands in about a trial centre, and the derivative
// of its 2theta with respect to that centre. Written once and compiled both for the host fit and for
// its device twin (BeamCenterBackgroundGPU), so the two read the same formula.
//
// The same formula is the same number only when both sides evaluate it the same way. The library
// atan2f differs between glibc and CUDA in the last bit, and the compilers fuse multiply-adds each
// in their own way; either moves a pixel within a rounding of a cell edge into the neighbouring cell
// (measured on 16 Mpx sweeps: ~30 of 6.5 million pixels, enough to move the fitted centre by up to
// 0.05 px). So the angles come from BackgroundAtan2 below and both translation units are compiled
// without contraction (geom_refinement/CMakeLists.txt), and the host and the device then agree to
// the bit.
#include <cmath>
#include <cstdint>
#include "../../common/JFJochMath.h"
#ifdef __CUDACC__
#define BACKGROUND_BAND_HD __host__ __device__ inline
#else
#define BACKGROUND_BAND_HD inline
#endif
struct BackgroundBand {
static constexpr int SECTORS = 36;
static constexpr int RADIAL_BINS = 120;
static constexpr int CELLS = RADIAL_BINS * SECTORS;
float rot[9]; // detector matrix, row major
float pixel_size; // mm
float distance; // mm
float tt_lo, tt_hi; // the band in 2theta
float d_tt; // width of one radial bin
double tan_lo, tan_hi; // the band in tan(2theta), widened for the quick rejection
};
// A panel of the image and its place on the plane (DetectorModule), in a form the device can hold.
struct BackgroundPanel {
int x0, y0, width, height;
double ox, oy, fx, fy, sx, sy;
};
// Plane position of image pixel (x, y) of panel p - DetectorModule::ImageToPlane, written here so that the
// host and the device evaluate it the same way.
BACKGROUND_BAND_HD void BackgroundPlanePoint(const BackgroundPanel &p, int x, int y, float &px, float &py) {
const double u = x - p.x0, v = y - p.y0;
px = static_cast<float>(p.ox + u * p.fx + v * p.sx);
py = static_cast<float>(p.oy + u * p.fy + v * p.sy);
}
// atan2(y, x) from IEEE operations alone - add, multiply, divide, square root, all correctly rounded on
// the host and on the device - so that, compiled without contraction (see CMakeLists.txt), the host
// and the device return the same bits. The library atan2f does not: glibc's and CUDA's differ in the
// last place. Two half-angle reductions take the argument below tan(pi/16), where eleven terms of the
// series leave an error under 1e-17.
BACKGROUND_BAND_HD double BackgroundAtan2(double y, double x) {
const double ax = x < 0 ? -x : x, ay = y < 0 ? -y : y;
if (ax == 0.0 && ay == 0.0)
return 0.0;
const bool swap = ay > ax;
double t = swap ? ax / ay : ay / ax;
t = t / (1.0 + sqrt(1.0 + t * t));
t = t / (1.0 + sqrt(1.0 + t * t));
const double t2 = t * t;
double series = 1.0 / 23.0;
for (int k = 21; k >= 1; k -= 2)
series = 1.0 / k - t2 * series;
double a = 4.0 * t * series;
if (swap) a = PI / 2 - a;
if (x < 0) a = PI - a;
return y < 0 ? -a : a;
}
// The cell of the pixel at (x, y) on the plane about (beam_x, beam_y), or -1 when it is outside the band;
// for a pixel in it, also the two components of the derivative of its 2theta with respect to the centre.
BACKGROUND_BAND_HD int BackgroundBandCell(const BackgroundBand &b, float x, float y, float beam_x, float beam_y,
float &jac_x, float &jac_y) {
const float *rot = b.rot;
const float u = (x - beam_x) * b.pixel_size;
const float v = (y - beam_y) * b.pixel_size;
const float lx = rot[0] * u + rot[1] * v + rot[2] * b.distance;
const float ly = rot[3] * u + rot[4] * v + rot[5] * b.distance;
const float lz = rot[6] * u + rot[7] * v + rot[8] * b.distance;
const float rho_sq = lx * lx + ly * ly;
// Most pixels lie outside the band. Those clearly outside it in tan(2theta) = rho / lz - by a
// margin far above float rounding - skip the square root and both atan2 below; every pixel the
// exact test would keep still reaches it.
if (lz > 0.0f) {
const double lz_sq = static_cast<double>(lz) * lz;
if (rho_sq < b.tan_lo * b.tan_lo * lz_sq || rho_sq > b.tan_hi * b.tan_hi * lz_sq)
return -1;
}
const float rho = sqrtf(rho_sq);
const float two_theta = static_cast<float>(BackgroundAtan2(rho, lz));
if (two_theta < b.tt_lo || two_theta >= b.tt_hi || rho == 0.0f)
return -1;
const float phi = static_cast<float>(BackgroundAtan2(ly, lx));
// Both bins are clamped: a pixel one float ulp below the top of the band divides to exactly
// RADIAL_BINS, which is one cell past the end of every accumulator.
int r_bin = static_cast<int>((two_theta - b.tt_lo) / b.d_tt);
r_bin = r_bin < 0 ? 0 : (r_bin > BackgroundBand::RADIAL_BINS - 1 ? BackgroundBand::RADIAL_BINS - 1 : r_bin);
int s_bin = static_cast<int>((phi + PI) / (2 * PI) * BackgroundBand::SECTORS);
s_bin = s_bin < 0 ? 0 : (s_bin > BackgroundBand::SECTORS - 1 ? BackgroundBand::SECTORS - 1 : s_bin);
// d(2theta)/d(beam), through the lab coordinate: the detector coordinate depends on the centre
// only as (x - beam_x), so moving the centre is moving the pixel.
const float denominator = rho * rho + lz * lz;
const float g_x = lz * lx / (rho * denominator);
const float g_y = lz * ly / (rho * denominator);
const float g_z = -rho / denominator;
jac_x = -b.pixel_size * (g_x * rot[0] + g_y * rot[3] + g_z * rot[6]);
jac_y = -b.pixel_size * (g_x * rot[1] + g_y * rot[4] + g_z * rot[7]);
return r_bin * BackgroundBand::SECTORS + s_bin;
}