Build Packages / Unit tests (push) Successful in 1h28m28s
Build Packages / build:windows:nocuda (push) Successful in 14m45s
Build Packages / build:windows:cuda (push) Successful in 13m13s
Build Packages / build:viewer-tgz:cpu (push) Successful in 6m47s
Build Packages / build:viewer-tgz:cuda (push) Successful in 7m22s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 13m52s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 14m16s
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 13m19s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 12m50s
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 14m40s
Build Packages / build:rpm (rocky8) (push) Successful in 11m18s
Build Packages / build:rpm (rocky9) (push) Successful in 12m4s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 11m55s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 11m22s
Build Packages / DIALS test (push) Successful in 13m37s
Build Packages / XDS test (durin plugin) (push) Successful in 8m47s
Build Packages / XDS test (JFJoch plugin) (push) Successful in 9m4s
Build Packages / XDS test (neggia plugin) (push) Successful in 7m45s
Build Packages / Generate python client (push) Successful in 34s
Build Packages / Build documentation (push) Successful in 1m4s
Build Packages / Create release (push) Skipped
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 7m16s
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: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
157 lines
6.4 KiB
C++
157 lines
6.4 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.157
|
|
* 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'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'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_ */
|