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