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Jungfraujoch/broker/gen/model/Indexing_settings.cpp
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v1.0.0.rc-161 (#71)
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>
2026-08-13 17:03:10 +02:00

456 lines
14 KiB
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/**
* Jungfraujoch
* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates. # License Clarification While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing. This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL. This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms.
*
* The version of the OpenAPI document: 1.0.0-rc.161
* Contact: filip.leonarski@psi.ch
*
* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
* https://openapi-generator.tech
* Do not edit the class manually.
*/
#include "Indexing_settings.h"
#include "Helpers.h"
#include <sstream>
namespace org::openapitools::server::model
{
Indexing_settings::Indexing_settings()
{
m_Fft_max_unit_cell_A = 250.0f;
m_Fft_min_unit_cell_A = 10.0f;
m_Fft_high_resolution_A = 2.0f;
m_Fft_num_vectors = 16384L;
m_Tolerance = 0.0f;
m_Thread_count = 0L;
m_Unit_cell_dist_tolerance = 0.05f;
m_Viable_cell_min_spots = 10L;
m_Index_ice_rings = false;
m_Rotation_indexing = false;
m_Rotation_indexing_min_angular_range_deg = 20.0f;
m_Rotation_indexing_angular_stride_deg = 0.5f;
m_Blocking = true;
}
void Indexing_settings::validate() const
{
std::stringstream msg;
if (!validate(msg))
{
throw org::openapitools::server::helpers::ValidationException(msg.str());
}
}
bool Indexing_settings::validate(std::stringstream& msg) const
{
return validate(msg, "");
}
bool Indexing_settings::validate(std::stringstream& msg, const std::string& pathPrefix) const
{
bool success = true;
const std::string _pathPrefix = pathPrefix.empty() ? "Indexing_settings" : pathPrefix;
/* Fft_max_unit_cell_A */ {
const float& value = m_Fft_max_unit_cell_A;
const std::string currentValuePath = _pathPrefix + ".fftMaxUnitCellA";
if (value < static_cast<float>(50))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 50;";
}
if (value > static_cast<float>(500))
{
success = false;
msg << currentValuePath << ": must be less than or equal to 500;";
}
}
/* Fft_min_unit_cell_A */ {
const float& value = m_Fft_min_unit_cell_A;
const std::string currentValuePath = _pathPrefix + ".fftMinUnitCellA";
if (value < static_cast<float>(5))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 5;";
}
if (value > static_cast<float>(40))
{
success = false;
msg << currentValuePath << ": must be less than or equal to 40;";
}
}
/* Fft_high_resolution_A */ {
const float& value = m_Fft_high_resolution_A;
const std::string currentValuePath = _pathPrefix + ".fftHighResolutionA";
if (value < static_cast<float>(0.5))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 0.5;";
}
if (value > static_cast<float>(6.0))
{
success = false;
msg << currentValuePath << ": must be less than or equal to 6.0;";
}
}
/* Fft_num_vectors */ {
const int64_t& value = m_Fft_num_vectors;
const std::string currentValuePath = _pathPrefix + ".fftNumVectors";
if (value < 128ll)
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 128;";
}
}
/* Tolerance */ {
const float& value = m_Tolerance;
const std::string currentValuePath = _pathPrefix + ".tolerance";
if (value < static_cast<float>(0.0))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 0.0;";
}
if (value > static_cast<float>(0.5))
{
success = false;
msg << currentValuePath << ": must be less than or equal to 0.5;";
}
}
/* Thread_count */ {
const int64_t& value = m_Thread_count;
const std::string currentValuePath = _pathPrefix + ".threadCount";
if (value < 1ll)
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 1;";
}
if (value > 64ll)
{
success = false;
msg << currentValuePath << ": must be less than or equal to 64;";
}
}
/* Unit_cell_dist_tolerance */ {
const float& value = m_Unit_cell_dist_tolerance;
const std::string currentValuePath = _pathPrefix + ".unitCellDistTolerance";
if (value < static_cast<float>(0.00010))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 0.00010;";
}
if (value > static_cast<float>(0.2001))
{
success = false;
msg << currentValuePath << ": must be less than or equal to 0.2001;";
}
}
/* Viable_cell_min_spots */ {
const int64_t& value = m_Viable_cell_min_spots;
const std::string currentValuePath = _pathPrefix + ".viableCellMinSpots";
if (value < 5ll)
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 5;";
}
}
/* Rotation_indexing_min_angular_range_deg */ {
const float& value = m_Rotation_indexing_min_angular_range_deg;
const std::string currentValuePath = _pathPrefix + ".rotationIndexingMinAngularRangeDeg";
if (value < static_cast<float>(1.0))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 1.0;";
}
}
/* Rotation_indexing_angular_stride_deg */ {
const float& value = m_Rotation_indexing_angular_stride_deg;
const std::string currentValuePath = _pathPrefix + ".rotationIndexingAngularStrideDeg";
if (value < static_cast<float>(0))
{
success = false;
msg << currentValuePath << ": must be greater than or equal to 0;";
}
}
return success;
}
bool Indexing_settings::operator==(const Indexing_settings& rhs) const
{
return
(getAlgorithm() == rhs.getAlgorithm())
&&
(getFftMaxUnitCellA() == rhs.getFftMaxUnitCellA())
&&
(getFftMinUnitCellA() == rhs.getFftMinUnitCellA())
&&
(getFftHighResolutionA() == rhs.getFftHighResolutionA())
&&
(getFftNumVectors() == rhs.getFftNumVectors())
&&
(getTolerance() == rhs.getTolerance())
&&
(getThreadCount() == rhs.getThreadCount())
&&
(getGeomRefinementAlgorithm() == rhs.getGeomRefinementAlgorithm())
&&
(getUnitCellDistTolerance() == rhs.getUnitCellDistTolerance())
&&
(getViableCellMinSpots() == rhs.getViableCellMinSpots())
&&
(isIndexIceRings() == rhs.isIndexIceRings())
&&
(isRotationIndexing() == rhs.isRotationIndexing())
&&
(getRotationIndexingMinAngularRangeDeg() == rhs.getRotationIndexingMinAngularRangeDeg())
&&
(getRotationIndexingAngularStrideDeg() == rhs.getRotationIndexingAngularStrideDeg())
&&
(isBlocking() == rhs.isBlocking())
;
}
bool Indexing_settings::operator!=(const Indexing_settings& rhs) const
{
return !(*this == rhs);
}
void to_json(nlohmann::json& j, const Indexing_settings& o)
{
j = nlohmann::json::object();
j["algorithm"] = o.m_Algorithm;
j["fft_max_unit_cell_A"] = o.m_Fft_max_unit_cell_A;
j["fft_min_unit_cell_A"] = o.m_Fft_min_unit_cell_A;
j["fft_high_resolution_A"] = o.m_Fft_high_resolution_A;
j["fft_num_vectors"] = o.m_Fft_num_vectors;
j["tolerance"] = o.m_Tolerance;
j["thread_count"] = o.m_Thread_count;
j["geom_refinement_algorithm"] = o.m_Geom_refinement_algorithm;
j["unit_cell_dist_tolerance"] = o.m_Unit_cell_dist_tolerance;
j["viable_cell_min_spots"] = o.m_Viable_cell_min_spots;
j["index_ice_rings"] = o.m_Index_ice_rings;
j["rotation_indexing"] = o.m_Rotation_indexing;
j["rotation_indexing_min_angular_range_deg"] = o.m_Rotation_indexing_min_angular_range_deg;
j["rotation_indexing_angular_stride_deg"] = o.m_Rotation_indexing_angular_stride_deg;
j["blocking"] = o.m_Blocking;
}
void from_json(const nlohmann::json& j, Indexing_settings& o)
{
j.at("algorithm").get_to(o.m_Algorithm);
j.at("fft_max_unit_cell_A").get_to(o.m_Fft_max_unit_cell_A);
j.at("fft_min_unit_cell_A").get_to(o.m_Fft_min_unit_cell_A);
j.at("fft_high_resolution_A").get_to(o.m_Fft_high_resolution_A);
j.at("fft_num_vectors").get_to(o.m_Fft_num_vectors);
j.at("tolerance").get_to(o.m_Tolerance);
j.at("thread_count").get_to(o.m_Thread_count);
j.at("geom_refinement_algorithm").get_to(o.m_Geom_refinement_algorithm);
j.at("unit_cell_dist_tolerance").get_to(o.m_Unit_cell_dist_tolerance);
j.at("viable_cell_min_spots").get_to(o.m_Viable_cell_min_spots);
j.at("index_ice_rings").get_to(o.m_Index_ice_rings);
j.at("rotation_indexing").get_to(o.m_Rotation_indexing);
j.at("rotation_indexing_min_angular_range_deg").get_to(o.m_Rotation_indexing_min_angular_range_deg);
j.at("rotation_indexing_angular_stride_deg").get_to(o.m_Rotation_indexing_angular_stride_deg);
j.at("blocking").get_to(o.m_Blocking);
}
org::openapitools::server::model::Indexing_algorithm Indexing_settings::getAlgorithm() const
{
return m_Algorithm;
}
void Indexing_settings::setAlgorithm(org::openapitools::server::model::Indexing_algorithm const& value)
{
m_Algorithm = value;
}
float Indexing_settings::getFftMaxUnitCellA() const
{
return m_Fft_max_unit_cell_A;
}
void Indexing_settings::setFftMaxUnitCellA(float const value)
{
m_Fft_max_unit_cell_A = value;
}
float Indexing_settings::getFftMinUnitCellA() const
{
return m_Fft_min_unit_cell_A;
}
void Indexing_settings::setFftMinUnitCellA(float const value)
{
m_Fft_min_unit_cell_A = value;
}
float Indexing_settings::getFftHighResolutionA() const
{
return m_Fft_high_resolution_A;
}
void Indexing_settings::setFftHighResolutionA(float const value)
{
m_Fft_high_resolution_A = value;
}
int64_t Indexing_settings::getFftNumVectors() const
{
return m_Fft_num_vectors;
}
void Indexing_settings::setFftNumVectors(int64_t const value)
{
m_Fft_num_vectors = value;
}
float Indexing_settings::getTolerance() const
{
return m_Tolerance;
}
void Indexing_settings::setTolerance(float const value)
{
m_Tolerance = value;
}
int64_t Indexing_settings::getThreadCount() const
{
return m_Thread_count;
}
void Indexing_settings::setThreadCount(int64_t const value)
{
m_Thread_count = value;
}
org::openapitools::server::model::Geom_refinement_algorithm Indexing_settings::getGeomRefinementAlgorithm() const
{
return m_Geom_refinement_algorithm;
}
void Indexing_settings::setGeomRefinementAlgorithm(org::openapitools::server::model::Geom_refinement_algorithm const& value)
{
m_Geom_refinement_algorithm = value;
}
float Indexing_settings::getUnitCellDistTolerance() const
{
return m_Unit_cell_dist_tolerance;
}
void Indexing_settings::setUnitCellDistTolerance(float const value)
{
m_Unit_cell_dist_tolerance = value;
}
int64_t Indexing_settings::getViableCellMinSpots() const
{
return m_Viable_cell_min_spots;
}
void Indexing_settings::setViableCellMinSpots(int64_t const value)
{
m_Viable_cell_min_spots = value;
}
bool Indexing_settings::isIndexIceRings() const
{
return m_Index_ice_rings;
}
void Indexing_settings::setIndexIceRings(bool const value)
{
m_Index_ice_rings = value;
}
bool Indexing_settings::isRotationIndexing() const
{
return m_Rotation_indexing;
}
void Indexing_settings::setRotationIndexing(bool const value)
{
m_Rotation_indexing = value;
}
float Indexing_settings::getRotationIndexingMinAngularRangeDeg() const
{
return m_Rotation_indexing_min_angular_range_deg;
}
void Indexing_settings::setRotationIndexingMinAngularRangeDeg(float const value)
{
m_Rotation_indexing_min_angular_range_deg = value;
}
float Indexing_settings::getRotationIndexingAngularStrideDeg() const
{
return m_Rotation_indexing_angular_stride_deg;
}
void Indexing_settings::setRotationIndexingAngularStrideDeg(float const value)
{
m_Rotation_indexing_angular_stride_deg = value;
}
bool Indexing_settings::isBlocking() const
{
return m_Blocking;
}
void Indexing_settings::setBlocking(bool const value)
{
m_Blocking = value;
}
} // namespace org::openapitools::server::model