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Jungfraujoch/broker/gen/model/Image_format_settings.h
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v1.0.0-rc.160 (#70)
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: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell.
* rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged.
* rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set.
* rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme.
* rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free.
* rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry.
* Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md.
* Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-07-19 09:39:28 +02:00

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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.160
* 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.
*/
/*
* Image_format_settings.h
*
*
*/
#ifndef Image_format_settings_H_
#define Image_format_settings_H_
#include <nlohmann/json.hpp>
namespace org::openapitools::server::model
{
/// <summary>
///
/// </summary>
class Image_format_settings
{
public:
Image_format_settings();
virtual ~Image_format_settings() = default;
/// <summary>
/// Validate the current data in the model. Throws a ValidationException on failure.
/// </summary>
void validate() const;
/// <summary>
/// Validate the current data in the model. Returns false on error and writes an error
/// message into the given stringstream.
/// </summary>
bool validate(std::stringstream& msg) const;
/// <summary>
/// Helper overload for validate. Used when one model stores another model and calls it's validate.
/// Not meant to be called outside that case.
/// </summary>
bool validate(std::stringstream& msg, const std::string& pathPrefix) const;
bool operator==(const Image_format_settings& rhs) const;
bool operator!=(const Image_format_settings& rhs) const;
/////////////////////////////////////////////
/// Image_format_settings members
/// <summary>
/// Enable summation of images to a given image_time If disabled images are saved according to original detector speed, but image count is adjusted
/// </summary>
bool isSummation() const;
void setSummation(bool const value);
/// <summary>
/// Place module read-out into their location on composed detector and extend multipixels
/// </summary>
bool isGeometryTransform() const;
void setGeometryTransform(bool const value);
/// <summary>
/// Convert pixel value in ADU to photon counts/energy Only affects JUNGFRAU detector
/// </summary>
bool isJungfrauConversion() const;
void setJungfrauConversion(bool const value);
/// <summary>
/// Used to convert energy deposited into pixel to counts If not provided incident_energy_keV is used
/// </summary>
float getJungfrauConversionFactorKeV() const;
void setJungfrauConversionFactorKeV(float const value);
bool jungfrauConversionFactorKeVIsSet() const;
void unsetJungfrau_conversion_factor_keV();
/// <summary>
/// Bit depth of resulting image (it doesn&#39;t affect the detector read-out value) If not provided value is adjusted automatically
/// </summary>
int64_t getBitDepthImage() const;
void setBitDepthImage(int64_t const value);
bool bitDepthImageIsSet() const;
void unsetBit_depth_image();
/// <summary>
/// Controls if pixels have signed output If not provided value is adjusted automatically
/// </summary>
bool isSignedOutput() const;
void setSignedOutput(bool const value);
bool signedOutputIsSet() const;
void unsetSigned_output();
/// <summary>
/// Mask 1 pixel on the module boundary
/// </summary>
bool isMaskModuleEdges() const;
void setMaskModuleEdges(bool const value);
/// <summary>
/// Mask multipixels on chip boundary
/// </summary>
bool isMaskChipEdges() const;
void setMaskChipEdges(bool const value);
/// <summary>
/// JUNGFRAU: mask pixels that don&#39;t operate in G0, but do operate in G1 and G1. This should be turned off for cases, where detector is operated at room temperature with long exposure time.
/// </summary>
bool isJungfrauMaskPixelsWithoutG0() const;
void setJungfrauMaskPixelsWithoutG0(bool const value);
bool jungfrauMaskPixelsWithoutG0IsSet() const;
void unsetJungfrau_mask_pixels_without_g0();
/// <summary>
/// Masked pixels are set to special value in the images produced by Jungfraujoch
/// </summary>
bool isApplyMask() const;
void setApplyMask(bool const value);
/// <summary>
/// Pixels with pedestal G0 RMS above the threshold are marked as masked pixels
/// </summary>
int64_t getJungfrauPedestalG0RmsLimit() const;
void setJungfrauPedestalG0RmsLimit(int64_t const value);
bool jungfrauPedestalG0RmsLimitIsSet() const;
void unsetJungfrau_pedestal_g0_rms_limit();
friend void to_json(nlohmann::json& j, const Image_format_settings& o);
friend void from_json(const nlohmann::json& j, Image_format_settings& o);
protected:
bool m_Summation;
bool m_Geometry_transform;
bool m_Jungfrau_conversion;
float m_Jungfrau_conversion_factor_keV;
bool m_Jungfrau_conversion_factor_keVIsSet;
int64_t m_Bit_depth_image;
bool m_Bit_depth_imageIsSet;
bool m_Signed_output;
bool m_Signed_outputIsSet;
bool m_Mask_module_edges;
bool m_Mask_chip_edges;
bool m_Jungfrau_mask_pixels_without_g0;
bool m_Jungfrau_mask_pixels_without_g0IsSet;
bool m_Apply_mask;
int64_t m_Jungfrau_pedestal_g0_rms_limit;
bool m_Jungfrau_pedestal_g0_rms_limitIsSet;
};
} // namespace org::openapitools::server::model
#endif /* Image_format_settings_H_ */