Files
Jungfraujoch/tests/BackgroundApertureTest.cpp
T
leonarski_f f199f23c54 Radial background: one mechanism for stills and rotation, decided per run on empty apertures (D5)
Wherever the correction is set for the whole run its curve is the frame's peak-excluded ring
background (the adaptive spot finder's, whole frame) and the ring's clip follows it - as stills have
done since integ-pal - now rotation too. One empty-aperture measurement (BackgroundAperture) decides
it for both workflows:

- The apertures' corrected difference is now taken as the integrator applies the correction: the
  clip follows the curve (each ring pixel's threshold raised by the curve's rise from the centre, in
  whole counts) as well as the kernel correction. Before, the tally clipped flat, so it measured a
  correction the engine never applies.
- Rotation measures the stencils the spot width can give it (r1 = 4, 5, 6 with the ring-area rule,
  RotationStencil) and decides on the one it gets, and separately on the pre-adaptive stencil the
  geometry pre-pass and the starvation guard return to.
- Stills: on wherever the corrected ring predicts the empty disk better (unchanged rule).
  Rotation: the frame's curve on every image only where it takes >= 10% of the apertures' mean
  square error away (ROTATION_RADIAL_MIN_GAIN); otherwise the existing per-image ice gate with the
  reflections' curve is left exactly as it was. Why a margin on rotation only: a still has no other
  correction, a sweep has one. Measured over 18 rotation sets (forced on every image): photon-counting
  sweeps gain 0.1-5% on the apertures (z 3-4) and lose ISa/anomalous signal when corrected
  (insulin, lysozyme, cytochrome c; 9yzk R-free +0.009 at 1.2%), as the earlier stills-rule trial
  found; the home-source CCD and smooth-ice runs gain 13-31%.

Result (CPU A/B vs 87684012f, 18 rotation sets): 12 .hkl byte-identical (every photon-counting
control without ice), 5uth R-free 0.210 -> 0.201 / ISa 10.4 -> 10.8, the ice set neutral; stills:
lcls242_s turns the correction on (the clip-following tally), R-free 0.2399 -> 0.2406.
No integration kernel changed; the tally is host code. Tests: BackgroundAperture_CorrectedClipFollowsTheCurve,
RadialHelps margins.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit dd3f3f2da39f5338e7dda1874bbdd535229bce98)
2026-10-24 07:27:12 +02:00

152 lines
7.0 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_test_macros.hpp>
#include <cmath>
#include <random>
#include "../image_analysis/bragg_integration/BackgroundAperture.h"
#include "../common/JFJochMath.h"
namespace {
constexpr int W = 600, H = 600;
// A background of `level` counts a pixel with Poisson noise, modulated by `ripple` (relative) with a
// period of 20 px along x - the structure a ring further from the disk reads wrong.
ImagePreprocessorBuffer Frame(double level, double ripple, uint32_t seed) {
std::mt19937 rng(seed);
ImagePreprocessorBuffer img(static_cast<size_t>(W) * H);
for (int y = 0; y < H; y++)
for (int x = 0; x < W; x++) {
std::poisson_distribution<int> p(level * (1.0 + ripple * std::sin(2.0 * PI * x / 20.0)));
img[static_cast<size_t>(y) * W + x] = p(rng);
}
return img;
}
const RingBackground no_rings({}, 0, 0.0f, 0.0f);
DiffractionGeometry Geometry() {
DiffractionGeometry g;
g.BeamX_pxl(300.0f).BeamY_pxl(300.0f).DetectorDistance_mm(60.0f).PixelSize_mm(0.075f).Wavelength_A(1.0f);
return g;
}
int BestR3(double level, double ripple) {
const auto r3 = background_aperture::CandidateR3(8.0f, 14.0f);
background_aperture::Tally tally;
for (uint32_t seed = 1; seed <= 4; seed++) {
auto img = Frame(level, ripple, seed);
background_aperture::MeasureFrame(img, W, H, {}, 6.0f, 8.0f, r3, 4.0f, 1.0f, no_rings, Geometry(),
DetectorModules(), tally);
}
REQUIRE(tally.apertures > 100);
CHECK(tally.apertures_radial == 0);
return static_cast<int>(r3[background_aperture::Best(tally.MeanSquare(false))]);
}
} // namespace
TEST_CASE("BackgroundAperture_CandidateR3", "[Integration]") {
const auto r3 = background_aperture::CandidateR3(8.0f, 14.0f);
REQUIRE(r3.size() == 5);
CHECK(r3.front() == 10.0f);
CHECK(r3.back() == 14.0f);
}
// A few counts a pixel on a flat background: the noise wins, and the widest ring is kept.
TEST_CASE("BackgroundAperture_FlatNoisyKeepsWidestRing", "[Integration]") {
CHECK(BestR3(0.5, 0.0) == 14);
}
// Thousands of counts a pixel on a background that varies over the stencil's own scale: the structure
// wins, and the narrowest ring is kept.
TEST_CASE("BackgroundAperture_StructuredBrightTakesNarrowestRing", "[Integration]") {
CHECK(BestR3(2000.0, 0.05) == 10);
}
// An aperture over an unreadable pixel is not used.
TEST_CASE("BackgroundAperture_SkipsUnreadablePixels", "[Integration]") {
const auto r3 = background_aperture::CandidateR3(8.0f, 14.0f);
auto img = Frame(1.0, 0.0, 7);
background_aperture::Tally all;
background_aperture::MeasureFrame(img, W, H, {}, 6.0f, 8.0f, r3, 4.0f, 1.0f, no_rings, Geometry(),
DetectorModules(), all);
for (size_t i = 0; i < static_cast<size_t>(W) * H; i += 97)
img[i] = INT32_MIN;
background_aperture::Tally masked;
background_aperture::MeasureFrame(img, W, H, {}, 6.0f, 8.0f, r3, 4.0f, 1.0f, no_rings, Geometry(),
DetectorModules(), masked);
CHECK(masked.apertures == 0);
CHECK(all.apertures > 0);
}
// A bright background that is a curved function of the radius alone: the radial correction, read off
// the frame's ring background, makes the ring predict the disk better than it does without it.
TEST_CASE("BackgroundAperture_RadialCorrectionHelpsOnARadialBackground", "[Integration]") {
const DiffractionGeometry g = Geometry();
const auto background = [](double r) { return 2000.0 + 0.2 * (r - 150.0) * (r - 150.0); };
std::mt19937 rng(3);
ImagePreprocessorBuffer img(static_cast<size_t>(W) * H);
for (int y = 0; y < H; y++)
for (int x = 0; x < W; x++) {
std::poisson_distribution<int> p(background(std::hypot(x - 300.0, y - 300.0)));
img[static_cast<size_t>(y) * W + x] = p(rng);
}
const float low_q = 0.05f, dq = 0.005f;
std::vector<float> profile(1000);
for (size_t i = 0; i < profile.size(); i++) {
const double q = low_q + (i + 0.5) * dq;
const double r = 60.0 / 0.075 * std::tan(2.0 * std::asin(q * 1.0 / (4.0 * PI)));
profile[i] = static_cast<float>(background(r));
}
const RingBackground rings(profile, static_cast<int32_t>(profile.size()), low_q, dq);
const auto r3 = background_aperture::CandidateR3(8.0f, 14.0f);
background_aperture::Tally tally;
// Unclipped: a gradient this steep would put the high side of the ring above a photon clip.
background_aperture::MeasureFrame(img, W, H, {}, 6.0f, 8.0f, r3, 0.0f, 1.0f, rings, g, DetectorModules(), tally);
REQUIRE(tally.apertures_radial == tally.apertures);
REQUIRE(tally.apertures > 100);
const auto plain = tally.MeanSquare(false), radial = tally.MeanSquare(true);
// The pre-scan's question: at the ring the plain differences choose, does the correction help.
const int best = background_aperture::Best(plain);
CHECK(radial[best] < 0.8 * plain[best]);
CHECK(background_aperture::RadialHelps(tally, best));
CHECK(background_aperture::RadialHelps(tally, best, background_aperture::ROTATION_RADIAL_MIN_GAIN));
CHECK(!background_aperture::RadialHelps(tally, best, 0.99));
// With the curvature taken out, the noise wins again and a wide ring is best.
CHECK(r3[background_aperture::Best(radial)] >= 12.0f);
}
// A background falling steeply away from the beam: the flat clip cuts the beam-side half of every ring
// and the ring reads low. The integrator's clip follows the curve when the correction is on, and so does
// the apertures' corrected measurement - which then predicts the disk far better.
TEST_CASE("BackgroundAperture_CorrectedClipFollowsTheCurve", "[Integration]") {
const DiffractionGeometry g = Geometry();
const auto background = [](double r) { return 50000.0 - 100.0 * r; };
std::mt19937 rng(5);
ImagePreprocessorBuffer img(static_cast<size_t>(W) * H);
for (int y = 0; y < H; y++)
for (int x = 0; x < W; x++) {
std::poisson_distribution<int> p(background(std::hypot(x - 300.0, y - 300.0)));
img[static_cast<size_t>(y) * W + x] = p(rng);
}
const float low_q = 0.05f, dq = 0.005f;
std::vector<float> profile(1000);
for (size_t i = 0; i < profile.size(); i++) {
const double q = low_q + (i + 0.5) * dq;
const double r = 60.0 / 0.075 * std::tan(2.0 * std::asin(q * 1.0 / (4.0 * PI)));
profile[i] = static_cast<float>(background(r));
}
const RingBackground rings(profile, static_cast<int32_t>(profile.size()), low_q, dq);
background_aperture::Tally tally;
background_aperture::MeasureFrame(img, W, H, {}, 6.0f, 8.0f, {14.0f}, 4.0f, 1.0f, rings, g, DetectorModules(),
tally);
REQUIRE(tally.apertures > 100);
const auto plain = tally.MeanSquare(false), radial = tally.MeanSquare(true);
CHECK(radial[0] < 0.1 * plain[0]);
CHECK(background_aperture::RadialHelps(tally, 0));
}