Files
Jungfraujoch/common/IndexingSettings.cpp
T
leonarski_fandClaude Opus 5 16bf3408f0 Address code-review findings; make detection limits detector-driven
One changeset, developed together in response to a review of this branch, so the
files carry several of the changes at once. Full test suite passes (733 cases).

Spot finding
- Split ImageSpotFinder into Detect() (flag strong pixels - the expensive
  per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with
  Run() = both. The per-image min-pix escalation now detects ONCE and repeats
  only the cheap extraction, instead of re-running the whole finder four times
  per frame as it did on the default path. It also keeps the winning attempt's
  spot list rather than re-extracting it, so the frame that is integrated is
  exactly the frame that was scored - which a GPU re-extract could not guarantee
  (float atomic ordering).
- spot_finding_time_s no longer swallows indexing time, and indexing_time_s now
  sums every escalation call instead of reporting only the last.

Detection limits follow the detector
- The azimuthal-integration upper q and the spot-finding high-resolution limit
  are now std::optional, in the C++ structs AND in the OpenAPI schema, and
  resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_
  recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a
  pixel outside that q range could never be strong - the integration range
  silently bounded what detection could see, regardless of the requested
  resolution limit. Regenerated the C++ and TypeScript clients; the viewer and
  the web frontend each gained a "to detector edge" switch.

Detection defaults are now per workflow (measured, not assumed)
- Stills: adaptive detection, min-pix chosen per image, no resolution clipping.
- Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit.
  On a 33-crystal rotation battery, adaptive detection helped four hard crystals
  but deterministically broke three (a lost space group, a halved indexing rate,
  a collapsed merge), and the detector-edge limit cost indexing on a strong
  rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and
  --no-adaptive-spots is new.

Indexer seed escalation
- Stop escalating once a seed's lattice explains >= 90% of the seed spots.
  Previously any frame with >= 80 spots always paid three indexer calls, online
  broker included.

Merge-consistency filter
- --min-image-cc gated on a per-image CC computed BEFORE the stills partiality
  post-refinement and never refreshed; the refiner now recomputes it, so the
  reported CC describes the data that are actually merged.
- Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the
  merge, the error model and MergeStats can no longer disagree about which
  images are in (the --scale path merged unfiltered while its statistics were
  filtered).

Per-image B-factor refinement (-B) removed
- Measured on four serial-stills datasets: it is a no-op where the per-image fit
  is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas
  +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on
  14-25% of images). It had also been silently DISCARDED since the partiality
  post-refinement landed - reported but not applied. Rather than fix and keep a
  knob with no demonstrated benefit, the flag and the whole image_scale_b_factor
  chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and
  read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs.
  ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS.
  (The Wilson per-image b_factor is a different quantity and stays.)

Stills partiality width now fits both of its components
- sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d*
  with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2
  on d*^2. The angular-only width is fitted over a d*^2-dense population, so it
  was pinned by the high-resolution edge and collapsed at low d*: median
  partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55%
  of them under the merge's partiality floor, and the survivors divided by those
  values - which inflated the merged low-resolution intensity scale 3.6x
  (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x,
  no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and
  R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining
  R-free are all blind to that ramp, which is why it survived earlier validation;
  the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged).

Removed dead code from add-then-remove churn
- Prediction-time "still partiality" (unreachable: no setter), the phantom
  IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the
  constant it always was), StillsPartialityRefine's caller-less Settings
  constructor and its reference to a long-gone env var, ProcessImage's unread
  bool return, an unused include, and a dead viewer overlay hook.

Also
- Viewer: the magnifier compared a QImage with itself, so its scene rect was set
  once ever and it could not pan into a larger dataset; the hover tail timer
  could fire after leaveEvent and resurrect the resolution readout outside the
  image.
- update_version.sh regenerated the frontend lock file BEFORE bumping the
  version (every release shipped an off-by-one lock), and did git rm/git add on
  a path that has not existed since the client moved to src/client - with no
  set -e, both failed silently.
- fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a
  redirect, not a test, so dkms add never ran.
- Unit tests for the adaptive-threshold host functions, which had none.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-07-27 09:07:00 +02:00

227 lines
7.0 KiB
C++

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "IndexingSettings.h"
#include "JFJochException.h"
#include "CUDAWrapper.h"
#include <cmath>
#define check_max(param, val, max) if ((val) > (max)) throw JFJochException(JFJochExceptionCategory::InputParameterAboveMax, param)
#define check_min(param, val, min) if ((val) < (min)) throw JFJochException(JFJochExceptionCategory::InputParameterBelowMin, param)
#define check_finite(param, val) if (!std::isfinite(val)) throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, param)
IndexingSettings::IndexingSettings() {
if (get_gpu_count() > 0)
algorithm = IndexingAlgorithmEnum::FFBIDX;
else
algorithm = IndexingAlgorithmEnum::None;
}
IndexingSettings &IndexingSettings::ViableCellMinSpots(int64_t input) {
check_min("ViableCellMinSpots", input, 6);
viable_cell_min_spots = input;
return *this;
}
int64_t IndexingSettings::GetViableCellMinSpots() const {
return viable_cell_min_spots;
}
IndexingSettings &IndexingSettings::Algorithm(IndexingAlgorithmEnum input) {
switch (input) {
case IndexingAlgorithmEnum::Auto:
case IndexingAlgorithmEnum::FFBIDX:
case IndexingAlgorithmEnum::FFT:
case IndexingAlgorithmEnum::FFTW:
case IndexingAlgorithmEnum::None:
algorithm = input;
break;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Invalid value for indexing algorithm enum parameter");
}
return *this;
}
IndexingSettings &IndexingSettings::FFT_MaxUnitCell_A(float input) {
check_finite("FFT indexing max unit cell (A)", input);
check_min("FFT indexing max unit cell (A)", input, 50);
check_max("FFT indexing max unit cell (A)", input, 500);
fft_max_unit_cell_A = input;
return *this;
}
IndexingSettings &IndexingSettings::FFT_MinUnitCell_A(float input) {
check_finite("FFT indexing min unit cell (A)", input);
check_min("FFT indexing min unit cell (A)", input, 5);
check_max("FFT indexing min unit cell (A)", input, 40);
fft_min_unit_cell_A = input;
return *this;
}
IndexingSettings & IndexingSettings::FFT_MaxAngle_deg(float input) {
check_finite("FFT indexing max angle (deg)", input);
check_min("FFT indexing max angle (deg)", input, 0);
check_max("FFT indexing max angle (deg)", input, 180);
fft_max_angle_deg = input;
return *this;
}
IndexingSettings & IndexingSettings::FFT_MinAngle_deg(float input) {
check_finite("FFT indexing min angle (deg)", input);
check_min("FFT indexing min angle (deg)", input, 0);
check_max("FFT indexing min angle (deg)", input, 180);
fft_min_angle_deg = input;
return *this;
}
float IndexingSettings::GetFFT_MinAngle_deg() const {
return fft_min_angle_deg;
}
float IndexingSettings::GetFFT_MaxAngle_deg() const {
return fft_max_angle_deg;
}
IndexingSettings &IndexingSettings::FFT_NumVectors(int64_t input) {
check_min("FFT indexing number of search vectors", input, 128);
fft_num_vectors = input;
return *this;
}
IndexingSettings &IndexingSettings::FFT_HighResolution_A(float input) {
check_finite("FFT indexing high resolution (A)", input);
check_min("FFT indexing high resolution (A)", input, 0.5);
check_max("FFT indexing high resolution (A)", input, 6.0);
fft_high_resolution_A = input;
return *this;
}
IndexingAlgorithmEnum IndexingSettings::GetAlgorithm() const {
return algorithm;
}
float IndexingSettings::GetFFT_MaxUnitCell_A() const {
return fft_max_unit_cell_A;
}
float IndexingSettings::GetFFT_MinUnitCell_A() const {
return fft_min_unit_cell_A;
}
int64_t IndexingSettings::GetFFT_NumVectors() const {
return fft_num_vectors;
}
float IndexingSettings::GetFFT_HighResolution_A() const {
return fft_high_resolution_A;
}
IndexingSettings &IndexingSettings::Tolerance(float input) {
check_min("Indexing tolerance", input, 0.0);
check_max("Indexing tolerance", input, 0.5);
indexing_tolerance = input;
return *this;
}
float IndexingSettings::GetTolerance() const {
return indexing_tolerance;
}
int64_t IndexingSettings::GetIndexingThreads() const {
return indexing_threads;
}
IndexingSettings &IndexingSettings::IndexingThreads(int64_t input) {
check_min("Indexing thread count", input, 1);
check_max("Indexing thread count", input, 64);
indexing_threads = input;
return *this;
}
IndexingSettings &IndexingSettings::UnitCellDistTolerance(float input) {
check_min("Relative unit cell distance tolerance vs. reference", input, 0.0001);
check_max("Relative unit cell distance tolerance vs. reference", input, 0.2001);
unit_cell_dist_tolerance_vs_reference = input;
return *this;
}
float IndexingSettings::GetUnitCellDistTolerance() const {
return unit_cell_dist_tolerance_vs_reference;
}
float IndexingSettings::GetUnitCellAngleTolerance_deg() const {
return unit_cell_angle_tolerance_deg;
}
GeomRefinementAlgorithmEnum IndexingSettings::GetGeomRefinementAlgorithm() const {
return refinement;
}
IndexingSettings &IndexingSettings::GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum input) {
refinement = input;
return *this;
}
IndexingSettings & IndexingSettings::IndexIceRings(bool input) {
index_ice_rings = input;
return *this;
}
IndexingSettings & IndexingSettings::RotationIndexing(bool input) {
enable_rotation_indexing = input;
return*this;
}
IndexingSettings & IndexingSettings::RotationIndexingMinAngularRange_deg(float input) {
check_finite("Rotation indexing minimum angular range (deg.)", input);
check_min("Rotation indexing minimum angular range (deg.)", input, 1.0);
rotation_indexing_min_angular_range_deg = input;
return *this;
}
IndexingSettings & IndexingSettings::RotationIndexingAngularStride_deg(float input) {
check_finite("Rotation indexing angular stride (deg.)", input);
check_min("Rotation indexing angular stride (deg.)", input, 0.0);
rotation_indexing_angular_stride_deg = input;
return *this;
}
bool IndexingSettings::GetRotationIndexing() const {
return enable_rotation_indexing;
}
float IndexingSettings::GetRotationIndexingMinAngularRange_deg() const {
return rotation_indexing_min_angular_range_deg;
}
float IndexingSettings::GetRotationIndexingAngularStride_deg() const {
return rotation_indexing_angular_stride_deg;
}
bool IndexingSettings::GetIndexIceRings() const {
return index_ice_rings;
}
bool IndexingSettings::GetBlockingBehavior() const {
return blocking_behavior;
}
IndexingSettings &IndexingSettings::BlockingBehavior(bool input) {
blocking_behavior = input;
return *this;
}
int64_t IndexingSettings::GetMaxExtraLattices() const {
return max_extra_lattices;
}
IndexingSettings &IndexingSettings::MaxExtraLattices(int64_t input) {
check_min("Max extra lattices", input, 0);
check_max("Max extra lattices", input, 10);
max_extra_lattices = input;
return *this;
}