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* `rugnux --model` adopts the model's space group as a label where the data were merged in its enantiomorph, instead of reindexing the reflections - which swapped I(+) with I(-). * `rugnux --model` warns, naming the atom, when the anomalous density at the model's atoms comes out inverted, which means the data and the model are in opposite hands. * `rugnux --model` writes an anomalous difference map (`<prefix>_anom.ccp4`) when the merge kept the Bijvoet split, and names the ten model atoms it peaks highest on as `ANOMALOUS_SITE_01`..`_10`. * `MEAN_ATOM_DENSITY_SIGMA` is read from the map by cubic rather than linear interpolation and comes out around a tenth higher; it is no longer comparable with the figure earlier versions printed. * `rugnux --model` reads an mmCIF coordinate file as well as a PDB one, gzipped or not, taking the format from the file's content rather than its name. * A model `rugnux --model` cannot use is reported as a `WARNING:` line in the results report instead of only in the log. * The rugnux results report has a `10. MODEL VALIDATION` section when `--model` was given; `REPORT_VERSION` is 4, `WARNINGS` moves to section 11 and no existing key changed. * The rugnux results report records how the run was invoked, what it cost and what it ran on: `COMMAND_LINE=`, `WALL_TIME=` and `GPU_COUNT=` / `GPU=`. * rugnux says which GPUs it can see before it starts processing. * `rugnux --export-unmerged` also writes `<prefix>_unmerged.mtz` on a `--no-merge` run, and is ignored on a run with no output prefix instead of writing a file called `_unmerged.mtz`. * `/start` asks the writer whether the run can be written before the detector is armed, so a run whose master file already exists, or whose output directory cannot be created, is refused up front with the writer's own message. This needs the TCP image stream or the built-in HDF5 writer; the ZeroMQ stream is unchanged. * A calibration that fails goes to `Error` carrying the reason instead of `Inactive`, so `/wait_till_done` and `/wait_until_running` report it; a cancelled calibration still goes to `Inactive`. * `/wait_till_done` answers 500 with the message when a collection ended in an error. A cancelled collection and a collection that only triggered a warning still answer 200. * A pending start failure is discarded by `/cancel` and `/deactivate`, as it already was by `/start` and `/initialize`. * `/scan_result` no longer reports the previous run's images after a collection that failed to start, or after `/deactivate`. * The TCP image stream protocol version is 4. `jfjoch_writer` and `jfjoch_broker` have to be of the same release, as before. Reviewed-on: #75
157 lines
6.4 KiB
C++
157 lines
6.4 KiB
C++
/**
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* Jungfraujoch
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* 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.
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*
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* The version of the OpenAPI document: 1.0.0-rc.165
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* Contact: filip.leonarski@psi.ch
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*
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* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
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* https://openapi-generator.tech
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* Do not edit the class manually.
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*/
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/*
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* Image_format_settings.h
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*
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*
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*/
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#ifndef Image_format_settings_H_
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#define Image_format_settings_H_
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#include <nlohmann/json.hpp>
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namespace org::openapitools::server::model
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{
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/// <summary>
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///
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/// </summary>
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class Image_format_settings
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{
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public:
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Image_format_settings();
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virtual ~Image_format_settings() = default;
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/// <summary>
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/// Validate the current data in the model. Throws a ValidationException on failure.
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/// </summary>
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void validate() const;
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/// <summary>
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/// Validate the current data in the model. Returns false on error and writes an error
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/// message into the given stringstream.
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/// </summary>
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bool validate(std::stringstream& msg) const;
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/// <summary>
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/// Helper overload for validate. Used when one model stores another model and calls it's validate.
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/// Not meant to be called outside that case.
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/// </summary>
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bool validate(std::stringstream& msg, const std::string& pathPrefix) const;
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bool operator==(const Image_format_settings& rhs) const;
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bool operator!=(const Image_format_settings& rhs) const;
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/////////////////////////////////////////////
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/// Image_format_settings members
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/// <summary>
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/// Enable summation of images to a given image_time If disabled images are saved according to original detector speed, but image count is adjusted
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/// </summary>
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bool isSummation() const;
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void setSummation(bool const value);
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/// <summary>
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/// Place module read-out into their location on composed detector and extend multipixels
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/// </summary>
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bool isGeometryTransform() const;
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void setGeometryTransform(bool const value);
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/// <summary>
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/// Convert pixel value in ADU to photon counts/energy Only affects JUNGFRAU detector
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/// </summary>
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bool isJungfrauConversion() const;
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void setJungfrauConversion(bool const value);
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/// <summary>
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/// Used to convert energy deposited into pixel to counts If not provided incident_energy_keV is used
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/// </summary>
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float getJungfrauConversionFactorKeV() const;
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void setJungfrauConversionFactorKeV(float const value);
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bool jungfrauConversionFactorKeVIsSet() const;
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void unsetJungfrau_conversion_factor_keV();
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/// <summary>
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/// Bit depth of resulting image (it doesn't affect the detector read-out value) If not provided value is adjusted automatically
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/// </summary>
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int64_t getBitDepthImage() const;
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void setBitDepthImage(int64_t const value);
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bool bitDepthImageIsSet() const;
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void unsetBit_depth_image();
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/// <summary>
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/// Controls if pixels have signed output If not provided value is adjusted automatically
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/// </summary>
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bool isSignedOutput() const;
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void setSignedOutput(bool const value);
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bool signedOutputIsSet() const;
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void unsetSigned_output();
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/// <summary>
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/// Mask 1 pixel on the module boundary
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/// </summary>
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bool isMaskModuleEdges() const;
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void setMaskModuleEdges(bool const value);
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/// <summary>
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/// Mask multipixels on chip boundary
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/// </summary>
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bool isMaskChipEdges() const;
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void setMaskChipEdges(bool const value);
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/// <summary>
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/// 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.
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/// </summary>
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bool isJungfrauMaskPixelsWithoutG0() const;
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void setJungfrauMaskPixelsWithoutG0(bool const value);
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bool jungfrauMaskPixelsWithoutG0IsSet() const;
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void unsetJungfrau_mask_pixels_without_g0();
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/// <summary>
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/// Masked pixels are set to special value in the images produced by Jungfraujoch
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/// </summary>
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bool isApplyMask() const;
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void setApplyMask(bool const value);
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/// <summary>
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/// Pixels with pedestal G0 RMS above the threshold are marked as masked pixels
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/// </summary>
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int64_t getJungfrauPedestalG0RmsLimit() const;
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void setJungfrauPedestalG0RmsLimit(int64_t const value);
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bool jungfrauPedestalG0RmsLimitIsSet() const;
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void unsetJungfrau_pedestal_g0_rms_limit();
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friend void to_json(nlohmann::json& j, const Image_format_settings& o);
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friend void from_json(const nlohmann::json& j, Image_format_settings& o);
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protected:
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bool m_Summation;
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bool m_Geometry_transform;
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bool m_Jungfrau_conversion;
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float m_Jungfrau_conversion_factor_keV;
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bool m_Jungfrau_conversion_factor_keVIsSet;
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int64_t m_Bit_depth_image;
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bool m_Bit_depth_imageIsSet;
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bool m_Signed_output;
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bool m_Signed_outputIsSet;
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bool m_Mask_module_edges;
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bool m_Mask_chip_edges;
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bool m_Jungfrau_mask_pixels_without_g0;
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bool m_Jungfrau_mask_pixels_without_g0IsSet;
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bool m_Apply_mask;
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int64_t m_Jungfrau_pedestal_g0_rms_limit;
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bool m_Jungfrau_pedestal_g0_rms_limitIsSet;
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};
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} // namespace org::openapitools::server::model
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#endif /* Image_format_settings_H_ */
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