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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
161 lines
8.1 KiB
C++
161 lines
8.1 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 <catch2/catch_test_macros.hpp>
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#include <catch2/matchers/catch_matchers_floating_point.hpp>
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#include <cmath>
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#include "../image_analysis/bragg_integration/BraggStencil.h"
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namespace {
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BraggStencilParams Params(float k_sigma, float bw_sigma = 0.002f) {
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BraggStencilParams p;
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p.beam_x = 400.0f;
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p.beam_y = 400.0f;
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p.r2 = 6.0f;
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p.r3 = 10.0f;
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p.bw_sigma = bw_sigma;
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p.k_sigma = k_sigma;
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p.max_grow = 2.0f * p.r3;
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return p;
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}
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} // namespace
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// The whole change rests on this: with no elongation asked for, the three squared distances the
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// integrator tests against must be the SAME BITS as the plain circular distance used before, so
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// that every pixel is classified exactly as it was, not merely nearly.
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TEST_CASE("BraggStencil_ZeroElongationIsExactlyCircular", "[Integration]") {
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const BraggStencilParams p = Params(0.0f); // a bandwidth, but k_sigma = 0
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for (float py = 0.0f; py < 800.0f; py += 37.0f)
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for (float px = 0.0f; px < 800.0f; px += 41.0f) {
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const BraggStencil s = MakeBraggStencil(px, py, p);
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REQUIRE(s.q_in == 0.0f);
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REQUIRE(s.q_out == 0.0f);
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for (int dy = -12; dy <= 12; ++dy)
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for (int dx = -12; dx <= 12; ++dx) {
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const auto d = BraggStencilDistances(s, static_cast<float>(dx), static_cast<float>(dy));
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const float circular = static_cast<float>(dx) * dx + static_cast<float>(dy) * dy;
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REQUIRE(d.signal == circular);
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REQUIRE(d.inner == circular);
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REQUIRE(d.outer == circular);
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}
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}
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}
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// A monochromatic beam has no streak, so nothing is elongated whatever k_sigma says - which is what
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// makes the feature inert on every monochromatic dataset rather than merely small.
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TEST_CASE("BraggStencil_MonochromaticIsInert", "[Integration]") {
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const BraggStencilParams p = Params(4.0f, 0.0f);
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for (float py = 0.0f; py < 800.0f; py += 53.0f)
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for (float px = 0.0f; px < 800.0f; px += 59.0f) {
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const BraggStencil s = MakeBraggStencil(px, py, p);
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REQUIRE(s.grow == 0.0f);
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REQUIRE(s.q_in == 0.0f);
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REQUIRE(s.q_out == 0.0f);
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}
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}
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// The elongated region really is the ellipse it claims: radial semi-axis r + grow, tangential r.
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TEST_CASE("BraggStencil_ElongatedSemiAxes", "[Integration]") {
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const BraggStencilParams p = Params(3.0f);
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for (float py = 120.0f; py < 800.0f; py += 91.0f)
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for (float px = 120.0f; px < 800.0f; px += 97.0f) {
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const BraggStencil s = MakeBraggStencil(px, py, p);
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const float grow = s.grow;
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REQUIRE(grow > 0.0f);
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REQUIRE(grow <= p.max_grow);
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REQUIRE(s.grow == BraggStencilGrow_px(s.r0, p)); // the kernel table indexes on this
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// On the radial axis the inner boundary sits at r2 + grow, the outer at r3 + grow.
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const auto rad_in = BraggStencilDistances(s, (p.r2 + grow) * s.ux, (p.r2 + grow) * s.uy);
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const auto rad_out = BraggStencilDistances(s, (p.r3 + grow) * s.ux, (p.r3 + grow) * s.uy);
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CHECK_THAT(rad_in.inner, Catch::Matchers::WithinRel(p.r2 * p.r2, 1e-4f));
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CHECK_THAT(rad_out.outer, Catch::Matchers::WithinRel(p.r3 * p.r3, 1e-4f));
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// Across it, at the untouched tangential half-widths r2 and r3. Testing on the exact
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// tangential axis would be a tautology - rad is 0 there, so q never enters - so the
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// point that matters is that the SAME offset is inside the region radially and outside
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// it tangentially. That is the anisotropy, and it fails if q is built from the wrong
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// radius or from a constant.
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const float probe = p.r2 + 0.5f * grow;
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const auto radial_probe = BraggStencilDistances(s, probe * s.ux, probe * s.uy);
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const auto tangent_probe = BraggStencilDistances(s, -probe * s.uy, probe * s.ux);
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CHECK(radial_probe.inner < p.r2 * p.r2); // still signal, the ring starts further out
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CHECK(tangent_probe.inner > p.r2 * p.r2); // already background across the streak
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const auto tan_in = BraggStencilDistances(s, -p.r2 * s.uy, p.r2 * s.ux);
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const auto tan_out = BraggStencilDistances(s, -p.r3 * s.uy, p.r3 * s.ux);
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CHECK_THAT(tan_in.inner, Catch::Matchers::WithinRel(p.r2 * p.r2, 1e-4f));
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CHECK_THAT(tan_out.outer, Catch::Matchers::WithinRel(p.r3 * p.r3, 1e-4f));
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}
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}
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// The bounding boxes the engines scan must contain the regions they classify - a box one pixel too
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// small silently drops background pixels on one side of every reflection, which no parity test
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// between two engines making the same mistake would catch.
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TEST_CASE("BraggStencil_BoundingBoxContainsRegion", "[Integration]") {
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const BraggStencilParams p = Params(3.0f);
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const float r2_sq = p.r2 * p.r2, r3_sq = p.r3 * p.r3;
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for (float py = 0.0f; py < 800.0f; py += 53.0f)
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for (float px = 0.0f; px < 800.0f; px += 59.0f) {
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const BraggStencil s = MakeBraggStencil(px, py, p);
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const int span = static_cast<int>(std::ceil(p.r3 + p.max_grow)) + 4;
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for (int dy = -span; dy <= span; ++dy)
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for (int dx = -span; dx <= span; ++dx) {
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const auto d = BraggStencilDistances(s, static_cast<float>(dx), static_cast<float>(dy));
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const float ax = std::fabs(static_cast<float>(dx)), ay = std::fabs(static_cast<float>(dy));
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// No slack: the offsets are integers from an exactly centred stencil, so the
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// extents bound them outright. A tolerance of a pixel here would accept a box
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// one pixel too small, which is the error this exists to catch.
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if (d.inner < r2_sq) {
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INFO("inner region outside its box at " << dx << "," << dy);
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REQUIRE(ax <= s.ex_in);
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REQUIRE(ay <= s.ey_in);
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}
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if (d.inner >= r2_sq && d.outer < r3_sq) {
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INFO("ring outside its box at " << dx << "," << dy);
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REQUIRE(ax <= s.ex_out);
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REQUIRE(ay <= s.ey_out);
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}
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}
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}
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}
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// The growth is capped, so a mis-declared bandwidth cannot run away with the bounding box.
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TEST_CASE("BraggStencil_GrowthIsCapped", "[Integration]") {
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BraggStencilParams p = Params(3.0f, 0.5f); // an absurdly declared bandwidth
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for (float r0 = 0.0f; r0 < 4000.0f; r0 += 17.0f)
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REQUIRE(BraggStencilGrow_px(r0, p) <= p.max_grow);
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const BraggStencil s = MakeBraggStencil(4000.0f, 4000.0f, p);
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REQUIRE(s.ex_out <= p.r3 + p.max_grow + 1e-3f);
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REQUIRE(s.ey_out <= p.r3 + p.max_grow + 1e-3f);
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}
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// The kernel table is indexed by the growth rounded to whole pixels, so the table has to have a row
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// for every index any reflection on the detector can produce. An off-by-one here is an out-of-range
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// read of k_diff - on the GPU, a device-side one.
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TEST_CASE("BraggStencil_KernelIndexInRange", "[Integration]") {
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for (const float k : {0.0f, 0.4f, 1.0f, 2.5f, 3.0f, 6.0f}) {
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const BraggStencilParams p = Params(k);
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const float r_max = std::hypot(800.0f - p.beam_x, 800.0f - p.beam_y);
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const int n_kern = static_cast<int>(std::lround(BraggStencilGrow_px(r_max, p))) + 1;
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REQUIRE(n_kern >= 1);
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for (float py = 0.0f; py <= 800.0f; py += 13.0f)
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for (float px = 0.0f; px <= 800.0f; px += 17.0f) {
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const BraggStencil s = MakeBraggStencil(px, py, p);
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const int idx = BraggStencilKernelIndex(s, n_kern);
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INFO("k " << k << " at " << px << "," << py << " grow " << s.grow);
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REQUIRE(idx >= 0);
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REQUIRE(idx < n_kern);
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// The clamp must never be what saves it: the table is sized so the row exists.
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REQUIRE(static_cast<int>(std::lround(s.grow)) == idx);
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}
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}
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}
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