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rotation indexer: fix sub-range crash, explicit angle, settings + guards

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Running rotation indexing on a sub-range (e.g. images 60-120) segfaulted: the
first pass passed the *global* image number to RotationIndexer::ProcessImage,
which indexes v_ (sized to the run's image count) -> out-of-bounds write.

- ProcessImage now takes an explicit mid-exposure angle (optional; falls back to
  the goniometer at the image index), so the indexer no longer assumes its slot
  index equals the goniometer image index. IndexAndRefine supplies it via
  RotationAngle(), matching the angle used for prediction. Added a bounds guard in
  ProcessImage so a bad index can never corrupt memory.
- JFJochProcess feeds the rotation indexer the local ordinal (not the global
  index), and shifts the goniometer (start += start_image*incr, incr *= stride,
  per-image wedge preserved) so local index i maps to the angle of original image
  start+i*stride - fixing rotation angles for the whole sub-range pipeline
  (prediction, refinement, output), not just the indexer.
- Expose "Rotation images" (number used for the first pass) in the job dialog,
  enabled when rotation indexing is on. (Count > available is already clamped by
  select_equally_spaced_image_ordinals.)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-06-22 15:59:21 +02:00
co-authored by Claude Opus 4.8
parent 67ad43a2b2
commit c86beeb393
7 changed files with 54 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
image_analysis/IndexAndRefine.cpp
+9 -2
View File
@@ -28,9 +28,16 @@ IndexAndRefine::IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool
unit_cells.resize(x.GetImageNum());
}
std::optional<float> IndexAndRefine::RotationAngle(int64_t image) const {
// Mid-exposure rotation angle for image index `image`, matching the angle used for prediction.
if (const auto g = experiment.GetGoniometer())
return g->GetAngle_deg(static_cast<float>(image)) + g->GetWedge_deg() / 2.0f;
return std::nullopt;
}
void IndexAndRefine::AddImageToRotationIndexer(DataMessage &msg) {
if (rotation_indexer)
rotation_indexer->ProcessImage(msg.number, msg.spots);
rotation_indexer->ProcessImage(msg.number, msg.spots, RotationAngle(msg.number));
}
IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetryRotation(DataMessage &msg) {
@@ -44,7 +51,7 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetryRotat
if (!result.has_value()) {
auto rot_cnt = rotation_indexer_counter.Process(msg.number);
if (rot_cnt.first)
rotation_indexer->ProcessImage(msg.number, msg.spots);
rotation_indexer->ProcessImage(msg.number, msg.spots, RotationAngle(msg.number));
if (rot_cnt.second)
rotation_indexer->RunIndexing();
result = rotation_indexer->GetLattice();
image_analysis/IndexAndRefine.h
+1
View File
@@ -82,6 +82,7 @@ class IndexAndRefine {
BraggPrediction &prediction,
const IndexingOutcome &outcome,
IntegrationOutcome &i_outcome);
std::optional<float> RotationAngle(int64_t image) const; // mid-exposure angle for the indexer
public:
IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer);
image_analysis/rotation_indexer/RotationIndexer.cpp
+10 -2
View File
@@ -13,6 +13,7 @@ RotationIndexer::RotationIndexer(const DiffractionExperiment &x, IndexerThreadPo
: experiment(x),
index_ice_rings(x.GetIndexingSettings().GetIndexIceRings()),
v_(experiment.GetImageNum()),
angle_deg_(experiment.GetImageNum()),
axis_(x.GetGoniometer()),
geom_(x.GetDiffractionGeometry()),
updated_geom_(geom_),
@@ -28,7 +29,7 @@ void RotationIndexer::RunIndexing() {
coords.reserve(max_spots_per_image * v_.size());
for (int i = 0; i < v_.size(); i++) {
const float angle_deg = axis_->GetAngle_deg(i) + axis_->GetWedge_deg() / 2.0f;
const float angle_deg = angle_deg_[i].value_or(axis_->GetAngle_deg(i) + axis_->GetWedge_deg() / 2.0f);
const auto rot = axis_->GetTransformationAngle(angle_deg);
for (const auto &s: v_[i])
@@ -115,19 +116,26 @@ void RotationIndexer::RunIndexing() {
}
}
void RotationIndexer::ProcessImage(int64_t image, const std::vector<SpotToSave> &spots) {
void RotationIndexer::ProcessImage(int64_t image, const std::vector<SpotToSave> &spots,
std::optional<float> angle_deg) {
std::unique_lock ul(m);
// For non-rotation just ignore the whole procedure
if (!axis_)
return;
// Guard: `image` is a slot in [0, image count); a bad index (e.g. a global number for a subset
// run) must not corrupt memory.
if (image < 0 || image >= static_cast<int64_t>(v_.size()))
return;
if (accumulated_spots >= max_spots)
return;
if (indexed_lattice)
return;
angle_deg_[image] = angle_deg;
v_[image].reserve(spots.size());
for (const auto &s: spots) {
image_analysis/rotation_indexer/RotationIndexer.h
+7 -1
View File
@@ -29,6 +29,9 @@ class RotationIndexer {
const bool index_ice_rings;
std::vector<std::vector<SpotToSave>> v_;
// Per-image rotation angle (mid-exposure, deg) supplied by the caller; falls back to the
// goniometer evaluated at the image index when not given.
std::vector<std::optional<float>> angle_deg_;
std::optional<GoniometerAxis> axis_;
const DiffractionGeometry geom_;
@@ -43,7 +46,10 @@ class RotationIndexer {
std::optional<CrystalLattice> indexed_lattice;
public:
RotationIndexer(const DiffractionExperiment& x, IndexerThreadPool& indexer);
void ProcessImage(int64_t image, const std::vector<SpotToSave>& spots);
// angle_deg is the image's mid-exposure rotation angle; if omitted, the goniometer angle at
// `image` is used (only valid when `image` is the goniometer's own image index).
void ProcessImage(int64_t image, const std::vector<SpotToSave>& spots,
std::optional<float> angle_deg = std::nullopt);
void RunIndexing();
std::optional<RotationIndexerResult> GetLattice() const;
void ForceLattice(const CrystalLattice& lattice);
process/JFJochProcess.cpp
+16 -1
View File
@@ -99,6 +99,21 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
if (full)
experiment_.Compression(CompressionAlgorithm::BSHUF_LZ4);
// The pipeline indexes images 0..N-1 within this run; if we process a sub-range/strided
// selection, shift the goniometer so local index i maps to the angle of original image
// start+i*stride (keeping the per-image rotation wedge), otherwise rotation angles would be
// wrong for any start_image != 0.
if (const auto g = experiment_.GetGoniometer();
g.has_value() && (start_image != 0 || config_.stride != 1)) {
const float incr = g->GetIncrement_deg();
GoniometerAxis shifted(g->GetName(),
g->GetStart_deg() + incr * static_cast<float>(start_image),
incr * static_cast<float>(config_.stride),
g->GetAxis(), g->GetHelicalStep());
shifted.ScreeningWedge(g->GetScreeningWedge().value_or(incr));
experiment_.Goniometer(shifted);
}
AzimuthalIntegrationMapping mapping(experiment_, pixel_mask_);
JFJochReceiverPlots plots;
@@ -165,7 +180,7 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
if (cancelled_) break;
const int image_idx = start_image + ordinal * config_.stride;
DataMessage msg{};
msg.number = image_idx;
msg.number = ordinal; // index into the rotation indexer (0..images_to_process-1)
msg.original_number = image_idx;
try {
if (config_.reuse_rotation_spots) {
viewer/windows/JFJochProcessingJobsWindow.cpp
+10
View File
@@ -138,14 +138,21 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
auto *rotation = new QCheckBox("Rotation indexing (two-pass)", &dlg);
rotation->setChecked(inputs.experiment.GetGoniometer().has_value());
auto *rotation_images = new QSpinBox(&dlg); // images used to find the rotation lattice
rotation_images->setRange(2, 1'000'000);
rotation_images->setValue(spec.rotation_images); // carries the default (30)
auto *scaling = new QCheckBox("Scale && merge", &dlg);
auto sync_full = [&] {
const bool full = mode->currentData().toInt() == static_cast<int>(ProcessMode::FullAnalysis);
rotation->setEnabled(full);
scaling->setEnabled(full);
rotation_images->setEnabled(full && rotation->isChecked());
};
connect(mode, &QComboBox::currentIndexChanged, &dlg, sync_full);
connect(rotation, &QCheckBox::toggled, &dlg, sync_full);
sync_full();
auto *form = new QFormLayout;
@@ -156,6 +163,7 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
form->addRow(save);
form->addRow("Output prefix", prefix);
form->addRow(rotation);
form->addRow("Rotation images", rotation_images);
form->addRow(scaling);
int result = 0;
@@ -186,6 +194,7 @@ int JFJochProcessingJobsWindow::askJob(const ReprocessingInputs &inputs, JobSpec
spec.save = save->isChecked();
spec.prefix = prefix->text();
spec.rotation = rotation->isEnabled() && rotation->isChecked();
spec.rotation_images = rotation_images->value();
spec.scaling = scaling->isEnabled() && scaling->isChecked();
}
return result;
@@ -202,6 +211,7 @@ ProcessConfig JFJochProcessingJobsWindow::buildConfig(const JobSpec &spec, const
if (spec.mode == ProcessMode::FullAnalysis) {
config.rotation_indexing = spec.rotation;
config.two_pass_rotation = true;
config.rotation_indexing_image_count = spec.rotation_images;
config.run_scaling = spec.scaling;
}
return config;
viewer/windows/JFJochProcessingJobsWindow.h
+1
View File
@@ -65,6 +65,7 @@ private:
bool save = true;
QString prefix;
bool rotation = false;
int rotation_images = 30; // images used to find the rotation lattice (first pass)
bool scaling = false;
};