Build Packages / Unit tests (push) Skipped
Build Packages / build:windows:nocuda (push) Successful in 11m6s
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 10m27s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 10m54s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 9m25s
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 10m5s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 11m33s
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 11m19s
Build Packages / build:rpm (rocky8) (push) Successful in 12m23s
Build Packages / build:rpm (rocky9) (push) Successful in 13m21s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 12m30s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 11m55s
Build Packages / DIALS test (push) Successful in 13m42s
Build Packages / XDS test (durin plugin) (push) Successful in 9m26s
Build Packages / XDS test (JFJoch plugin) (push) Successful in 6m41s
Build Packages / XDS test (neggia plugin) (push) Successful in 6m12s
Build Packages / Generate python client (push) Successful in 19s
Build Packages / Build documentation (push) Successful in 52s
Build Packages / Create release (push) Skipped
Build Packages / build:viewer-tgz:cpu (push) Successful in 5m29s
Build Packages / build:viewer-tgz:cuda (push) Successful in 6m12s
Build Packages / build:windows:cuda (push) Successful in 18m36s
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: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
129 lines
5.1 KiB
C++
129 lines
5.1 KiB
C++
/**
|
|
* 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.159
|
|
* 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_buffer_status.h
|
|
*
|
|
*
|
|
*/
|
|
|
|
#ifndef Image_buffer_status_H_
|
|
#define Image_buffer_status_H_
|
|
|
|
|
|
#include <vector>
|
|
#include <nlohmann/json.hpp>
|
|
|
|
namespace org::openapitools::server::model
|
|
{
|
|
|
|
/// <summary>
|
|
///
|
|
/// </summary>
|
|
class Image_buffer_status
|
|
{
|
|
public:
|
|
Image_buffer_status();
|
|
virtual ~Image_buffer_status() = 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_buffer_status& rhs) const;
|
|
bool operator!=(const Image_buffer_status& rhs) const;
|
|
|
|
/////////////////////////////////////////////
|
|
/// Image_buffer_status members
|
|
|
|
/// <summary>
|
|
/// Smallest image number available in the buffer
|
|
/// </summary>
|
|
int64_t getMinImageNumber() const;
|
|
void setMinImageNumber(int64_t const value);
|
|
/// <summary>
|
|
/// Largest image number available in the buffer
|
|
/// </summary>
|
|
int64_t getMaxImageNumber() const;
|
|
void setMaxImageNumber(int64_t const value);
|
|
/// <summary>
|
|
/// Image numbers currently present in the buffer.
|
|
/// </summary>
|
|
std::vector<int64_t> getImageNumbers() const;
|
|
void setImageNumbers(std::vector<int64_t> const value);
|
|
/// <summary>
|
|
/// Number of slots in the image buffer. This number, compared to number of images in data collection and frame rate will determine \"retention\" rate of the image buffer.
|
|
/// </summary>
|
|
int64_t getTotalSlots() const;
|
|
void setTotalSlots(int64_t const value);
|
|
/// <summary>
|
|
/// Slots available for the data collection
|
|
/// </summary>
|
|
int64_t getAvailableSlots() const;
|
|
void setAvailableSlots(int64_t const value);
|
|
/// <summary>
|
|
/// Number of slots in the image buffer that are currently in preparation for sending.
|
|
/// </summary>
|
|
int64_t getInPreparationSlots() const;
|
|
void setInPreparationSlots(int64_t const value);
|
|
/// <summary>
|
|
/// Number of slots in the image buffer that are currently sending/writing data.
|
|
/// </summary>
|
|
int64_t getInSendingSlots() const;
|
|
void setInSendingSlots(int64_t const value);
|
|
/// <summary>
|
|
/// Counter of changes in the image buffer - either new start message or new image added. For optimization one can only load new images/datasets from the HTTP if this value changes. Counter is optional as it was not implemented in older versions to avoid breaking change
|
|
/// </summary>
|
|
int64_t getCurrentCounter() const;
|
|
void setCurrentCounter(int64_t const value);
|
|
bool currentCounterIsSet() const;
|
|
void unsetCurrent_counter();
|
|
|
|
friend void to_json(nlohmann::json& j, const Image_buffer_status& o);
|
|
friend void from_json(const nlohmann::json& j, Image_buffer_status& o);
|
|
protected:
|
|
int64_t m_Min_image_number;
|
|
|
|
int64_t m_Max_image_number;
|
|
|
|
std::vector<int64_t> m_Image_numbers;
|
|
|
|
int64_t m_Total_slots;
|
|
|
|
int64_t m_Available_slots;
|
|
|
|
int64_t m_In_preparation_slots;
|
|
|
|
int64_t m_In_sending_slots;
|
|
|
|
int64_t m_Current_counter;
|
|
bool m_Current_counterIsSet;
|
|
|
|
};
|
|
|
|
} // namespace org::openapitools::server::model
|
|
|
|
#endif /* Image_buffer_status_H_ */
|