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v1.0.0-rc.147 (#57)
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Browse Source 
This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.

* jfjoch_viewer: Add reciprocal space viewer
* jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset
* jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress)

Reviewed-on: #57
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This commit was merged in pull request #57.
This commit is contained in:
leonarski_f
2026-06-02 11:49:24 +02:00
committed by leonarski_f
parent fc68a9baed
commit 75de40f52b
162 changed files with 2651 additions and 851 deletions
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tests/XtalOptimizerTest.cpp
+20 -15
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@@ -39,7 +39,7 @@ TEST_CASE("XtalOptimizer") {
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
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;
@@ -94,7 +94,7 @@ TEST_CASE("XtalOptimizer_NoBeamCenter") {
xtal_opt.max_time = 30.0;
auto start = std::chrono::high_resolution_clock::now();
REQUIRE(XtalOptimizer(xtal_opt, spots));
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;
@@ -145,7 +145,7 @@ TEST_CASE("XtalOptimizer_orthorombic") {
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));
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;
@@ -197,7 +197,7 @@ TEST_CASE("XtalOptimizer_triclinic") {
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));
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;
@@ -250,7 +250,7 @@ TEST_CASE("XtalOptimizer_tetragonal") {
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));
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;
@@ -302,7 +302,7 @@ TEST_CASE("XtalOptimizer_hexagonal") {
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);
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;
@@ -356,7 +356,7 @@ TEST_CASE("XtalOptimizer_hexagonal_unconstrained") {
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));
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;
@@ -415,7 +415,7 @@ TEST_CASE("XtalOptimizer_cubic") {
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));
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;
@@ -469,7 +469,7 @@ TEST_CASE("XtalOptimizer_monoclinic") {
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));
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;
@@ -578,11 +578,13 @@ TEST_CASE("XtalOptimizer_rotation") {
.ewald_dist_cutoff = 0.002
};
std::vector<SpotToSave> spots;
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 < 10; ++img) {
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);
@@ -599,7 +601,7 @@ TEST_CASE("XtalOptimizer_rotation") {
s.intensity = 1.0f; // minimal positive value
s.ice_ring = false;
s.indexed = true;
spots.push_back(s);
spots[img].push_back(s);
}
}
@@ -663,11 +665,14 @@ TEST_CASE("XtalOptimizer_refine_rotation_axis") {
.ewald_dist_cutoff = 0.002
};
std::vector<SpotToSave> spots;
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 < 10; ++img) {
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);
@@ -684,7 +689,7 @@ TEST_CASE("XtalOptimizer_refine_rotation_axis") {
s.phi = angle_deg;
s.ice_ring = false;
s.indexed = true;
spots.push_back(s);
spots.at(img).push_back(s);
}
}