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Jungfraujoch/tests/XtalOptimizerTest.cpp
T
leonarski_fandClaude Opus 5 9c19646f6a refine: fit the direction of the goniometer axis, not its length 
The residual applies angle_rad * |rot_vec| and rot_vec is a free three-vector, so the first pass has
been fitting a goniometer rotation SCALE nobody asked for. GoniometerAxis::Axis() then normalises it
away on write-back, and RotationIndexer scores the candidate with the normalised axis - so the cell
that won the fit is judged under a rotation model the fit did not use. Measured over 43 rotation
datasets: the length reaches 1.2%, and the fit-vs-score disagreement a median 0.124 deg and up to
6.19 deg of goniometer angle, against rocking widths of 0.05-0.36 deg. That score picks the lattice
class, which nothing later revisits.

The fitted length is not a usable measurement of anything either: on synthetic data it recovers 54%
of a known scale error, repeated first passes on one dataset disagree with each other in sign, 26 of
43 datasets disagree with themselves, and on the one dataset with a proven 1.3% stage fault it comes
out negative. It is absorbing other systematics. The rotation scale is measured properly, once, with
cross-validation and gates, in PostRefine.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
2026-09-01 18:36:32 +02:00

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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include <iostream>
#include "../image_analysis/geom_refinement/XtalOptimizer.h"
#include "../image_analysis/bragg_prediction/BraggPrediction.h"
TEST_CASE("XtalOptimizer") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,40,80,90,90,90);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.max_time = 30.0;
xtal_opt.latt = CrystalLattice(40.2,39.4,80.2, 90,91, 89);
xtal_opt.geom.BeamX_pxl(1010).BeamY_pxl(995).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.05);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.05);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
}
TEST_CASE("XtalOptimizer_NoBeamCenter") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,50,80,90,95,90);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(40.2,49.4,80.2, 90,94, 89);
xtal_opt.geom.BeamX_pxl(999.8).BeamY_pxl(1000.2).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.refine_beam_center = false;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - 999.8) < 0.01);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - 1000.2) < 0.01);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
}
TEST_CASE("XtalOptimizer_orthorombic") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,50,80,90,90,90);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(40.2,49.6,80.3, 90,91, 89);
xtal_opt.geom.BeamX_pxl(1005).BeamY_pxl(997).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.max_time = 30.0;
xtal_opt.crystal_system = gemmi::CrystalSystem::Orthorhombic;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.02);
CHECK(fabs(uc_o.beta - 90) < 0.02);
CHECK(fabs(uc_o.gamma - 90) < 0.02);
}
TEST_CASE("XtalOptimizer_triclinic") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,55,120,95,97,100);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001,
};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(40.1,54.9,121, 95,97, 99.5);
xtal_opt.geom.BeamX_pxl(997).BeamY_pxl(1005).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
xtal_opt.max_time = 36.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.5);
CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
}
TEST_CASE("XtalOptimizer_tetragonal") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,40,80,90,90,90);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(40.6,39.3,80.5, 90,91, 89);
xtal_opt.geom.BeamX_pxl(1010).BeamY_pxl(995).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Tetragonal;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.5);
CHECK(fabs(uc_o.alpha - 90) < 0.02);
CHECK(fabs(uc_o.beta - 90) < 0.02);
CHECK(fabs(uc_o.gamma - 90) < 0.02);
}
TEST_CASE("XtalOptimizer_hexagonal") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,40,70,90,90,120);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(39.5,39.8,70.1, 90,90, 119.5);
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Hexagonal;
xtal_opt.max_time = 60.0;
auto start = std::chrono::high_resolution_clock::now();
bool ret = XtalOptimizer(xtal_opt, {spots});
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
REQUIRE(ret);
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta
<< " " << uc_o.gamma << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.02);
CHECK(fabs(uc_o.beta - 90) < 0.01);
CHECK(fabs(uc_o.gamma - 120) < 0.01);
}
TEST_CASE("XtalOptimizer_hexagonal_unconstrained") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(40,40,70,90,90,120);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(39.9,39.8,70.1, 90,90, 120);
xtal_opt.geom.BeamX_pxl(1002).BeamY_pxl(998).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_i = latt_i.GetUnitCell();
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta
<< " " << uc_o.gamma << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.3);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.3);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.1);
CHECK(fabs(uc_o.beta - 90) < 0.1);
CHECK(fabs(uc_o.gamma - 120) < 0.1);
}
TEST_CASE("XtalOptimizer_cubic") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(Coord(40,0,0),
Coord(0, 40 / sqrt(2), -40 / sqrt(2)),
Coord(0, 40 / sqrt(2), 40 / sqrt(2)));
auto uc_i = latt_i.GetUnitCell();
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(Coord(39,0,0),
Coord(0, 39.5 / sqrt(2), -40.5 / sqrt(2)),
Coord(0, 39.2 / sqrt(2), 39.7 / sqrt(2)));
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Cubic;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.02);
CHECK(fabs(uc_o.beta - 90) < 0.02);
CHECK(fabs(uc_o.gamma - 90) < 0.02);
}
TEST_CASE("XtalOptimizer_monoclinic") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
CrystalLattice latt_i(50,60,70,90,115,90);
auto uc_i = latt_i.GetUnitCell();
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.001
};
BraggPrediction prediction;
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
std::vector<SpotToSave> spots;
for (int i = 0; i < count; ++i) {
auto refl = prediction.GetReflections().at(i);
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(49.5, 60.5, 69.8, 90, 113.5, 90);
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, {spots}));
auto end = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
<< " microseconds" << std::endl;
auto uc_o = xtal_opt.latt.GetUnitCell();
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta << " " << uc_o.gamma << std::endl;
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2);
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
CHECK(fabs(uc_o.alpha - 90) < 0.05);
CHECK(fabs(uc_o.beta - uc_i.beta) < 0.05);
CHECK(fabs(uc_o.gamma - 90) < 0.05);
}
TEST_CASE("XtalOptimizer_rotation") {
// Geometry
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
// Base lattice (non-pathological)
CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
auto uc_ref = latt_base.GetUnitCell();
// Rotation axis: around X with 3 deg per image
GoniometerAxis axis("omega", 0.0f, 3.0f, Coord(1,0,0), std::nullopt);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.002
};
size_t nimages = 10;
std::vector<std::vector<SpotToSave>> spots(nimages);
BraggPrediction prediction;
// Predict reflections for images at 0-30 deg.
for (int img = 0; img < nimages; ++img) {
// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
for (int i = 0; i < n; ++i) {
const auto& r = prediction.GetReflections().at(i);
SpotToSave s{};
s.x = r.predicted_x;
s.y = r.predicted_y;
s.image = img; // provide image index for rotation-aware refinement
s.phi = angle_deg;
s.intensity = 1.0f; // minimal positive value
s.ice_ring = false;
s.indexed = true;
spots[img].push_back(s);
}
}
// Seed slightly perturbed geometry and lattice; provide rotation axis for refinement.
// The beam-centre component PARALLEL to the spindle (here X, the rotation axis) is a gauge-weak
// direction that XtalOptimizer now deliberately restrains toward the header rather than refining
// freely (see the BeamComponentPrior in XtalOptimizer.cpp). So only the perpendicular component
// (Y) is seeded off-truth to exercise beam-centre recovery; X is seeded at its true value.
// The distance is seeded at its true value too: XtalOptimizer does not refine it - the rotation
// post-refinement fits it globally instead, where the cell is held fixed and the two are no longer
// degenerate - so a distance seeded off-truth here would simply be absorbed by the cell.
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
xtal_opt.geom.BeamX_pxl(1000).BeamY_pxl(997).DetectorDistance_mm(200.0)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.axis = axis;
xtal_opt.min_spots = 200;
xtal_opt.refine_beam_center = true;
xtal_opt.refine_detector_angles = false;
xtal_opt.max_time = 30.0;
auto t0 = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto t1 = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer (rotation 4 images) took "
<< std::chrono::duration_cast<std::chrono::microseconds>(t1 - t0).count()
<< " microseconds" << std::endl;
const auto uc_out = xtal_opt.latt.GetUnitCell();
// Geometry checks
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2f);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2f);
// Lattice checks
CHECK(fabsf(uc_ref.a - uc_out.a) < 0.2f);
CHECK(fabsf(uc_ref.b - uc_out.b) < 0.2f);
CHECK(fabsf(uc_ref.c - uc_out.c) < 0.4f);
CHECK(fabsf(uc_ref.alpha - uc_out.alpha) < 0.2f);
CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
}
TEST_CASE("XtalOptimizer_refine_rotation_axis") {
// Geometry
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000)
.BeamY_pxl(1000)
.PoniRot1_rad(0.01)
.PoniRot2_rad(0.02)
.DetectorDistance_mm(200);
// Base lattice (non-pathological)
CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
auto uc_ref = latt_base.GetUnitCell();
// Rotation axis: around X with 3 deg per image
GoniometerAxis axis("omega", 0.0f, 3.0f, Coord(1,0,0), std::nullopt);
BraggPredictionSettings prediction_settings{
.high_res_A = 1.5,
.ewald_dist_cutoff = 0.002
};
BraggPrediction prediction;
const size_t nimages = 10;
std::vector<std::vector<SpotToSave>> spots(nimages);
// Predict reflections for images at 0-30 deg.
for (int img = 0; img < nimages; ++img) {
// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
for (int i = 0; i < n; ++i) {
const auto& r = prediction.GetReflections().at(i);
SpotToSave s{};
s.x = r.predicted_x;
s.y = r.predicted_y;
s.image = img; // provide image index for rotation-aware refinement
s.intensity = 1.0f; // minimal positive value
s.phi = angle_deg;
s.ice_ring = false;
s.indexed = true;
spots.at(img).push_back(s);
}
}
// Seed slightly perturbed geometry and lattice; provide rotation axis for refinement
XtalOptimizerData xtal_opt{};
xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
xtal_opt.geom.BeamX_pxl(1003).BeamY_pxl(997).DetectorDistance_mm(200.0)
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.axis = GoniometerAxis("omega", 0.0f, 3.0f,
Coord(0.8, 0.05, 0.05).Normalize(),
std::nullopt);
xtal_opt.min_spots = 200;
xtal_opt.refine_beam_center = true;
xtal_opt.refine_detector_angles = false;
xtal_opt.refine_rotation_axis = true;
xtal_opt.max_time = 30.0;
auto t0 = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
auto t1 = std::chrono::high_resolution_clock::now();
std::cout << "XtalOptimizer (rotation 4 images) took "
<< std::chrono::duration_cast<std::chrono::microseconds>(t1 - t0).count()
<< " microseconds" << std::endl;
const auto uc_out = xtal_opt.latt.GetUnitCell();
// Geometry checks
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2f);
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2f);
// Lattice checks
CHECK(fabsf(uc_ref.a - uc_out.a) < 0.2f);
CHECK(fabsf(uc_ref.b - uc_out.b) < 0.2f);
CHECK(fabsf(uc_ref.c - uc_out.c) < 0.3f);
CHECK(fabsf(uc_ref.alpha - uc_out.alpha) < 0.2f);
CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
CHECK(fabsf(xtal_opt.axis->GetAxis().x - 1.0) < 0.01f);
CHECK(fabsf(xtal_opt.axis->GetAxis().y) < 0.01f);
CHECK(fabsf(xtal_opt.axis->GetAxis().z) < 0.01f);
}
// The rotation residual applies `angle_rad * |rot_vec|`, so the goniometer axis block must be
// constrained to unit length or the solve also fits a rotation SCALE that GoniometerAxis::Axis()
// then normalises away. Generate spots whose true rotation is k times the angles the optimizer is
// handed - k = 1 for a healthy goniometer, k = 1.01 for a stage that turned 1 % further than it was
// commanded - and check the axis DIRECTION and the cell come back either way. (Before the axis block
// was put on the unit sphere, the free length absorbed part of that 1 %: on this noise-free data it
// reached only 1.00538 of the 1.01 it would have had to reach to be a measurement.)
TEST_CASE("XtalOptimizer_rotation_axis_direction_only") {
DiffractionExperiment exp_i;
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(1000).BeamY_pxl(1000)
.DetectorDistance_mm(200);
const CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
const auto uc_ref = latt_base.GetUnitCell();
const double k_true = GENERATE(1.000, 1.010);
// The angles the FILE records. The stage actually turned k_true times as far.
GoniometerAxis nominal("omega", 0.0f, 3.0f, Coord(1, 0, 0), std::nullopt);
BraggPredictionSettings prediction_settings{.high_res_A = 1.5, .ewald_dist_cutoff = 0.002};
BraggPrediction prediction;
const size_t nimages = 40;
std::vector<std::vector<SpotToSave>> spots(nimages);
for (size_t img = 0; img < nimages; ++img) {
const float nominal_deg = nominal.GetAngle_deg(img) + nominal.GetWedge_deg() / 2.0f;
const RotMatrix rot = nominal.GetTransformationAngle(static_cast<float>(nominal_deg * k_true));
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
for (int i = 0; i < n; ++i) {
const auto &r = prediction.GetReflections().at(i);
SpotToSave s{};
s.x = r.predicted_x;
s.y = r.predicted_y;
s.image = static_cast<int32_t>(img);
s.intensity = 1.0f;
s.phi = nominal_deg;
s.indexed = true;
spots.at(img).push_back(s);
}
}
XtalOptimizerData xtal_opt{};
xtal_opt.latt = latt_base;
xtal_opt.geom.BeamX_pxl(1000).BeamY_pxl(1000).DetectorDistance_mm(200.0);
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
xtal_opt.axis = GoniometerAxis("omega", 0.0f, 3.0f, Coord(0.999, 0.02, 0.02).Normalize(),
std::nullopt);
xtal_opt.min_spots = 200;
xtal_opt.refine_beam_center = true;
xtal_opt.refine_detector_angles = true;
xtal_opt.refine_rotation_axis = true;
xtal_opt.max_iterations = 200;
REQUIRE(XtalOptimizer(xtal_opt, spots));
const Coord axis_out = xtal_opt.axis->GetAxis();
CHECK(std::fabs(axis_out.Length() - 1.0f) < 1e-5f);
CHECK(std::fabs(axis_out.x - 1.0f) < 0.01f);
CHECK(std::fabs(axis_out.y) < 0.01f);
CHECK(std::fabs(axis_out.z) < 0.01f);
const auto uc_out = xtal_opt.latt.GetUnitCell();
CHECK(std::fabs(uc_ref.a - uc_out.a) < 0.2f);
CHECK(std::fabs(uc_ref.b - uc_out.b) < 0.2f);
CHECK(std::fabs(uc_ref.c - uc_out.c) < 0.3f);
}
// --- helpers for lattice sanity tests ---
#include <Eigen/Dense>
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