leonarski_fandClaude Opus 5
a7d3ada3ab
Until now nothing in the tree said what analysis a run performed. The answer was composed
at each site out of four independent scalars - the detector type, two separate "spot finding
off" switches, an indexing flag and a rotation flag - so what was configured and what
actually ran were different things, and no single place could be read to find out which.
AnalysisMode {None, MXRotation, MXStills, Azint, Grid, PowderCalibration} is that statement,
in common/ because all three programs configure the DiffractionExperiment that carries it.
AnalysisSettings sits on the experiment beside IndexingSettings, outside the DatasetSettings
member, which is the one thing a /start replaces wholesale - so the mode is persistent by
construction rather than by a rule someone has to remember.
The mode does not label a run, it decides it. AnalysisModeStages() is a table - modes as
rows, pipeline stages as columns - and every gate reads that table instead of testing the
mode: spot finding in DiffractionExperiment::IsSpotFindingEnabled, indexing (and with it
prediction and integration, which never run without a lattice) in one gate inside
IndexAndRefine that serves all three front ends, azimuthal integration where the CPU engine
is built. Two rows carry a judgement worth reviewing: powder calibration keeps spot finding,
because --calibration spots fits the pooled spots; grid does not index, because a raster is
thousands of frames and the per-image scoring it ranks on deliberately avoids an indexer that
fires on ice.
There is deliberately no Auto value. GetIndexingAlgorithm() resolves Auto at read time, which
is exactly why an indexing setting cannot be read back off the configuration; removing that
kind of implicitness is the point here, so the mode getter stays a plain accessor. MXStills
is the default because None would silently switch analysis off on every deployment whose
configuration predates the field.
Rotation MX is absent from the OpenAPI schema rather than present and refused: jfjoch_broker
has no rotation analysis path, so the REST and configuration-file routes cannot express it at
all. The shared enum can still carry the value from elsewhere, so CheckAnalysisSettingsOnline
refuses it on both routes with a message naming rugnux. A sweep collected under an MX mode is
not refused - collecting rotation data online is normal and live spot counts are useful - but
it is said out loud in the log, since the mistake worth preventing is the silence about what
was done to it, not the acquisition.
Powder calibration forces azimuthal integration onto the CPU and supplies 32 sectors where
fewer than four were asked for. The FPGA integration core holds 2048 bins in total, so 32
sectors would leave 64 q bins - far too coarse to fit a ring. Frame rate is what this costs
and a calibration exposure does not need it.
The two existing "no analysis" switches, per-dataset dataset_settings.spot_finding and
persistent SpotFindingSettings::enable, are interfaces in too many places to remove now. They
are marked deprecated in the schema and in both headers, and the mode takes precedence over
them: a mode that analyses no spots wins outright, while under a mode that does find spots
they remain the finer control. The precedence is written where it is enforced.
rugnux's ProcessMode is gone, replaced by the shared enum; RugnuxMode stays as the CLI
spelling layer and no existing spelling changes. --mode gains mx_rotation and mx_stills, which
are spellings of -R and --force-still rather than new switches; plain mx still chooses between
them from the goniometer. scale keeps no shared counterpart, since it runs no analysis over
images at all.
The mode reaches the CBOR start message and /entry/MX/analysis_mode in the HDF5 master, so a
written file records which analysis produced it. It is read back as provenance only - what a
stored file was produced by is not what the next run should do.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
1317 lines
58 KiB
C++
1317 lines
58 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "../common/JFJochMath.h"
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#include "OpenAPIConvert.h"
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// From https://en.cppreference.com/w/cpp/string/byte/tolower
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std::string str_tolower(std::string s) {
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std::transform(s.begin(), s.end(), s.begin(), [](unsigned char c){ return std::tolower(c); });
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return s;
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}
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SpotFindingSettings Convert(const org::openapitools::server::model::Spot_finding_settings &input) {
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SpotFindingSettings ret{};
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ret.signal_to_noise_threshold = input.getSignalToNoiseThreshold();
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ret.photon_count_threshold = input.getPhotonCountThreshold();
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ret.min_pix_per_spot = input.getMinPixPerSpot();
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ret.max_pix_per_spot = input.getMaxPixPerSpot();
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// Both limits are optional and unset means "no limit at that end". A value of 0 has meant the same
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// thing since rc.161 and clients still send it that way, so fold it into the unset case here - the
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// analysis code then has exactly one spelling for "no limit" and no zero to special-case.
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if (input.highResolutionLimitIsSet() && input.getHighResolutionLimit() > 0)
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ret.high_resolution_limit = input.getHighResolutionLimit();
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if (input.lowResolutionLimitIsSet() && input.getLowResolutionLimit() > 0)
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ret.low_resolution_limit = input.getLowResolutionLimit();
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ret.enable = input.isEnable();
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ret.indexing = input.isIndexing();
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ret.quick_integration = input.isQuickIntegration();
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ret.cutoff_spot_count_low_res = input.getHighResolutionLimitForSpotCountLowRes();
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ret.ice_ring_width_Q_recipA = input.getIceRingWidthQRecipA();
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if (input.highResGapQRecipAIsSet())
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ret.high_res_gap_Q_recipA = input.getHighResGapQRecipA();
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if (input.adaptiveThresholdIsSet())
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ret.adaptive_threshold = input.isAdaptiveThreshold();
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if (input.falsePixelsPerFrameIsSet())
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ret.false_pixels_per_frame = input.getFalsePixelsPerFrame();
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return ret;
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}
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org::openapitools::server::model::Spot_finding_settings Convert(const SpotFindingSettings &input) {
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org::openapitools::server::model::Spot_finding_settings ret;
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ret.setSignalToNoiseThreshold(input.signal_to_noise_threshold);
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ret.setPhotonCountThreshold(input.photon_count_threshold);
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ret.setMinPixPerSpot(input.min_pix_per_spot.value_or(2));
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ret.setMaxPixPerSpot(input.max_pix_per_spot);
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if (input.high_resolution_limit.has_value())
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ret.setHighResolutionLimit(input.high_resolution_limit.value());
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if (input.low_resolution_limit.has_value())
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ret.setLowResolutionLimit(input.low_resolution_limit.value());
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ret.setEnable(input.enable);
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ret.setIndexing(input.indexing);
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ret.setHighResolutionLimitForSpotCountLowRes(input.cutoff_spot_count_low_res);
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ret.setQuickIntegration(input.quick_integration);
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ret.setIceRingWidthQRecipA(input.ice_ring_width_Q_recipA);
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if (input.high_res_gap_Q_recipA.has_value())
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ret.setHighResGapQRecipA(input.high_res_gap_Q_recipA.value());
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ret.setAdaptiveThreshold(input.adaptive_threshold);
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ret.setFalsePixelsPerFrame(input.false_pixels_per_frame);
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return ret;
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}
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org::openapitools::server::model::Measurement_statistics Convert(const MeasurementStatistics &input) {
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org::openapitools::server::model::Measurement_statistics ret{};
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if (!input.file_prefix.empty())
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ret.setFilePrefix(input.file_prefix);
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ret.setExperimentGroup(input.experiment_group);
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ret.setImagesExpected(input.images_expected);
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ret.setImagesCollected(input.images_collected);
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ret.setImagesSent(input.images_sent);
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ret.setImagesDiscardedLossyCompression(input.images_skipped);
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ret.setMaxImageNumberSent(input.max_image_number_sent);
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if (input.collection_efficiency)
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ret.setCollectionEfficiency(input.collection_efficiency.value());
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if (input.compression_ratio)
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ret.setCompressionRatio(input.compression_ratio.value());
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ret.setCancelled(input.cancelled);
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if (input.max_receive_delay)
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ret.setMaxReceiverDelay(input.max_receive_delay.value());
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ret.setDetectorWidth(input.detector_width);
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ret.setDetectorHeight(input.detector_height);
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ret.setDetectorPixelDepth(input.detector_pixel_depth);
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if (input.roi_beam_npixel)
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ret.setRoiBeamPixels(input.roi_beam_npixel.value());
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if (input.roi_beam_sum)
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ret.setRoiBeamSum(input.roi_beam_sum.value());
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if (input.error_pixels)
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ret.setErrorPixels(input.error_pixels.value());
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if (input.saturated_pixels)
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ret.setSaturatedPixels(input.saturated_pixels.value());
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if (input.indexing_rate)
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ret.setIndexingRate(input.indexing_rate.value());
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if (input.bkg_estimate)
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ret.setBkgEstimate(input.bkg_estimate.value());
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ret.setUnitCell(input.unit_cell);
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ret.setRunNumber(input.run_number);
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if (input.images_written)
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ret.setImagesWritten(input.images_written.value());
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return ret;
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}
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DetectorTiming Convert(const org::openapitools::server::model::Detector_timing& input) {
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switch (input.getValue()) {
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case org::openapitools::server::model::Detector_timing::eDetector_timing::AUTO:
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return DetectorTiming::Auto;
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case org::openapitools::server::model::Detector_timing::eDetector_timing::TRIGGER:
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return DetectorTiming::Trigger;
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case org::openapitools::server::model::Detector_timing::eDetector_timing::BURST:
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return DetectorTiming::Burst;
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case org::openapitools::server::model::Detector_timing::eDetector_timing::GATED:
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return DetectorTiming::Gated;
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default:
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case org::openapitools::server::model::Detector_timing::eDetector_timing::INVALID_VALUE_OPENAPI_GENERATED:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "invalid input");
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}
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}
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org::openapitools::server::model::Detector_timing Convert(DetectorTiming input) {
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org::openapitools::server::model::Detector_timing val;
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switch (input) {
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case DetectorTiming::Auto:
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val.setValue(org::openapitools::server::model::Detector_timing::eDetector_timing::AUTO);
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break;
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case DetectorTiming::Trigger:
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val.setValue(org::openapitools::server::model::Detector_timing::eDetector_timing::TRIGGER);
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break;
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case DetectorTiming::Burst:
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val.setValue(org::openapitools::server::model::Detector_timing::eDetector_timing::BURST);
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break;
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case DetectorTiming::Gated:
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val.setValue(org::openapitools::server::model::Detector_timing::eDetector_timing::GATED);
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "invalid input");
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}
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return val;
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}
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DetectorSettings Convert(const org::openapitools::server::model::Detector_settings &input) {
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DetectorSettings ret{};
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if (input.countTimeUsIsSet())
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ret.FrameTime(std::chrono::microseconds(input.getFrameTimeUs()),
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std::chrono::microseconds(input.getCountTimeUs()));
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else
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ret.FrameTime(std::chrono::microseconds(input.getFrameTimeUs()));
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ret.InternalGeneratorEnable(input.isInternalFrameGenerator());
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ret.InternalGeneratorImages(input.getInternalFrameGeneratorImages());
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ret.DetectorDelay(std::chrono::nanoseconds(input.getDetectorTriggerDelayNs()));
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ret.StorageCells(input.getJungfrauStorageCellCount());
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ret.StorageCellDelay(std::chrono::nanoseconds(input.getJungfrauStorageCellDelayNs()));
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ret.FixGainG1(input.isJungfrauFixedGainG1());
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ret.UseGainHG0(input.isJungfrauUseGainHg0());
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ret.PedestalG0Frames(input.getJungfrauPedestalG0Frames());
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ret.PedestalG1Frames(input.getJungfrauPedestalG1Frames());
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ret.PedestalG2Frames(input.getJungfrauPedestalG2Frames());
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ret.PedestalMinImageCount(input.getJungfrauPedestalMinImageCount());
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if (input.eigerBitDepthIsSet())
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ret.EigerBitDepth(input.getEigerBitDepth());
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if (input.eigerThresholdKeVIsSet())
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ret.EigerThreshold_keV(input.getEigerThresholdKeV());
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if (input.timingIsSet())
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ret.Timing(Convert(input.getTiming()));
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else
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ret.Timing(DetectorTiming::Trigger);
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return ret;
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}
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org::openapitools::server::model::Detector_settings Convert(const DetectorSettings &input) {
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org::openapitools::server::model::Detector_settings ret{};
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ret.setFrameTimeUs(std::chrono::round<std::chrono::microseconds>(
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std::chrono::duration<float>(input.GetFrameTime())).count());
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if (input.GetCountTime().has_value())
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ret.setCountTimeUs(std::chrono::round<std::chrono::microseconds>(
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std::chrono::duration<float>(input.GetCountTime().value())
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).count());
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ret.setDetectorTriggerDelayNs(input.GetDetectorDelay().count());
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ret.setInternalFrameGeneratorImages(input.GetInternalGeneratorImages());
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ret.setInternalFrameGenerator(input.IsInternalGeneratorEnable());
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ret.setJungfrauStorageCellCount(input.GetStorageCells());
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ret.setJungfrauFixedGainG1(input.IsFixGainG1());
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ret.setJungfrauUseGainHg0(input.IsUseGainHG0());
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ret.setJungfrauPedestalG0Frames(input.GetPedestalG0Frames());
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ret.setJungfrauPedestalG1Frames(input.GetPedestalG1Frames());
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ret.setJungfrauPedestalG2Frames(input.GetPedestalG2Frames());
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ret.setJungfrauPedestalMinImageCount(input.GetPedestalMinImageCount());
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ret.setJungfrauStorageCellDelayNs(input.GetStorageCellDelay().count());
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if (input.GetEigerThreshold_keV().has_value())
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ret.setEigerThresholdKeV(input.GetEigerThreshold_keV().value());
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if (input.GetEigerBitDepth().has_value())
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ret.setEigerBitDepth(input.GetEigerBitDepth().value());
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ret.setTiming(Convert(input.GetTiming()));
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return ret;
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}
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org::openapitools::server::model::Broker_status Convert(const BrokerStatus& input) {
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org::openapitools::server::model::Broker_status ret;
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switch (input.state) {
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case JFJochState::Inactive:
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ret.setState("Inactive");
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break;
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case JFJochState::Idle:
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ret.setState("Idle");
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break;
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case JFJochState::Measuring:
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ret.setState("Measuring");
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break;
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case JFJochState::Error:
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ret.setState("Error");
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break;
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case JFJochState::Busy:
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ret.setState("Busy");
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break;
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case JFJochState::Calibration:
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ret.setState("Pedestal");
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break;
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}
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if (input.message.has_value())
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ret.setMessage(input.message.value());
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switch (input.message_severity) {
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case BrokerStatus::MessageSeverity::Info:
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ret.setMessageSeverity("info");
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break;
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case BrokerStatus::MessageSeverity::Success:
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ret.setMessageSeverity("success");
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break;
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case BrokerStatus::MessageSeverity::Warning:
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ret.setMessageSeverity("warning");
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break;
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default:
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ret.setMessageSeverity("error");
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break;
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}
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if (input.progress.has_value())
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ret.setProgress(input.progress.value());
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ret.setGpuCount(input.gpu_count);
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ret.setBrokerVersion(input.broker_version);
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return ret;
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}
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org::openapitools::server::model::Calibration_statistics_inner Convert(const JFCalibrationModuleStatistics& input) {
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org::openapitools::server::model::Calibration_statistics_inner output;
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output.setModuleNumber(input.module_number);
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output.setMaskedPixels(input.bad_pixels);
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output.setStorageCellNumber(input.storage_cell_number);
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output.setGainG0Mean(input.gain_g0_mean);
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output.setGainG1Mean(input.gain_g1_mean);
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output.setGainG2Mean(input.gain_g2_mean);
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output.setPedestalG0Mean(input.pedestal_g0_mean);
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output.setPedestalG1Mean(input.pedestal_g1_mean);
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output.setPedestalG2Mean(input.pedestal_g2_mean);
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return output;
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}
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std::vector<org::openapitools::server::model::Calibration_statistics_inner> Convert(const std::vector<JFCalibrationModuleStatistics>& input) {
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std::vector<org::openapitools::server::model::Calibration_statistics_inner> ret;
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for (const auto &i: input)
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ret.push_back(Convert(i));
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return ret;
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}
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org::openapitools::server::model::Instrument_metadata Convert(const InstrumentMetadata& input) {
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org::openapitools::server::model::Instrument_metadata output;
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output.setInstrumentName(input.GetInstrumentName());
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output.setSourceName(input.GetSourceName());
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output.setSourceType(input.GetSourceType());
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output.setPulsedSource(input.IsPulsedSource());
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output.setElectronSource(input.IsElectronSource());
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return output;
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}
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InstrumentMetadata Convert(const org::openapitools::server::model::Instrument_metadata &input) {
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InstrumentMetadata output;
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output.InstrumentName(input.getInstrumentName())
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.SourceName(input.getSourceName())
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.SourceType(input.getSourceType())
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.PulsedSource(input.isPulsedSource())
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.ElectronSource(input.isElectronSource());
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return output;
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}
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org::openapitools::server::model::Detector_state Convert(DetectorState input) {
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org::openapitools::server::model::Detector_state ret;
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switch (input) {
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case DetectorState::IDLE:
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ret.setValue(org::openapitools::server::model::Detector_state::eDetector_state::IDLE);
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break;
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case DetectorState::ERROR:
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ret.setValue(org::openapitools::server::model::Detector_state::eDetector_state::ERROR);
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break;
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case DetectorState::BUSY:
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ret.setValue(org::openapitools::server::model::Detector_state::eDetector_state::BUSY);
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break;
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case DetectorState::WAITING:
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ret.setValue(org::openapitools::server::model::Detector_state::eDetector_state::WAITING);
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break;
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default:
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case DetectorState::NOT_CONNECTED:
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ret.setValue(org::openapitools::server::model::Detector_state::eDetector_state::NOT_CONNECTED);
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break;
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}
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return ret;
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}
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org::openapitools::server::model::Detector_power_state Convert(DetectorPowerState input) {
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org::openapitools::server::model::Detector_power_state ret;
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switch (input) {
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case DetectorPowerState::ON:
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ret.setValue(org::openapitools::server::model::Detector_power_state::eDetector_power_state::POWERON);
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break;
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case DetectorPowerState::PARTIAL:
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ret.setValue(org::openapitools::server::model::Detector_power_state::eDetector_power_state::PARTIAL);
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break;
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default:
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case DetectorPowerState::OFF:
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ret.setValue(org::openapitools::server::model::Detector_power_state::eDetector_power_state::POWEROFF);
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break;
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}
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return ret;
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}
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org::openapitools::server::model::Detector_status Convert(const DetectorStatus &input) {
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org::openapitools::server::model::Detector_status output;
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output.setServerVersion(input.detector_server_version);
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output.setNumberOfTriggersLeft(input.remaining_triggers);
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output.setFpgaTempDegC(input.temperature_fpga_degC);
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output.setHighVoltageV(input.high_voltage_V);
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output.setPowerchip(Convert(input.power_state));
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output.setState(Convert(input.detector_state));
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return output;
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}
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org::openapitools::server::model::Detector_type Convert(const DetectorType &input) {
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org::openapitools::server::model::Detector_type dt;
|
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switch (input) {
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case DetectorType::EIGER:
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dt.setValue(org::openapitools::server::model::Detector_type::eDetector_type::EIGER);
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break;
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|
case DetectorType::JUNGFRAU:
|
|
dt.setValue(org::openapitools::server::model::Detector_type::eDetector_type::JUNGFRAU);
|
|
break;
|
|
case DetectorType::DECTRIS:
|
|
dt.setValue(org::openapitools::server::model::Detector_type::eDetector_type::DECTRIS);
|
|
break;
|
|
}
|
|
return dt;
|
|
}
|
|
|
|
org::openapitools::server::model::Detector_list Convert(const DetectorList &input) {
|
|
org::openapitools::server::model::Detector_list ret;
|
|
std::vector<org::openapitools::server::model::Detector_list_element> dets;
|
|
for (int i = 0; i < input.detector.size(); i++) {
|
|
org::openapitools::server::model::Detector_list_element d;
|
|
d.setId(i);
|
|
d.setDescription(input.detector[i].description);
|
|
d.setNmodules(input.detector[i].nmodules);
|
|
d.setHeight(input.detector[i].height);
|
|
d.setWidth(input.detector[i].width);
|
|
d.setSerialNumber(input.detector[i].serial_number);
|
|
d.setBaseIpv4Addr(input.detector[i].base_ipv4_addr);
|
|
d.setUdpInterfaceCount(input.detector[i].udp_interface_count);
|
|
d.setMinFrameTimeNs(input.detector[i].min_frame_time.count());
|
|
d.setMinCountTimeNs(input.detector[i].min_count_time.count());
|
|
d.setReadoutTimeNs(input.detector[i].readout_time.count());
|
|
d.setPixelSizeMm(input.detector[i].pixel_size_mm);
|
|
d.setType(Convert(input.detector[i].detector_type));
|
|
dets.emplace_back(std::move(d));
|
|
}
|
|
ret.setDetectors(dets);
|
|
ret.setCurrentId(input.current_id);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Plots Convert(const MultiLinePlot& input) {
|
|
std::vector<org::openapitools::server::model::Plot> tmp(input.GetPlots().size());
|
|
for (int i = 0; i < input.GetPlots().size(); i++) {
|
|
tmp[i].setTitle(input.GetPlots()[i].title);
|
|
tmp[i].setX(input.GetPlots()[i].x);
|
|
tmp[i].setY(input.GetPlots()[i].y);
|
|
tmp[i].setZ(input.GetPlots()[i].z);
|
|
}
|
|
|
|
org::openapitools::server::model::Plots output;
|
|
output.setPlot(tmp);
|
|
|
|
org::openapitools::server::model::Plot_unit_x unit;
|
|
switch (input.GetUnits()) {
|
|
case MultiLinePlotUnits::ImageNumber:
|
|
unit.setValue(org::openapitools::server::model::Plot_unit_x::ePlot_unit_x::IMAGE_NUMBER);
|
|
break;
|
|
case MultiLinePlotUnits::Angle_deg:
|
|
unit.setValue(org::openapitools::server::model::Plot_unit_x::ePlot_unit_x::ANGLE_DEG);
|
|
break;
|
|
case MultiLinePlotUnits::Q_recipA:
|
|
unit.setValue(org::openapitools::server::model::Plot_unit_x::ePlot_unit_x::Q_RECIPA);
|
|
break;
|
|
case MultiLinePlotUnits::ADU:
|
|
unit.setValue(org::openapitools::server::model::Plot_unit_x::ePlot_unit_x::ADU);
|
|
break;
|
|
case MultiLinePlotUnits::d_A:
|
|
unit.setValue(org::openapitools::server::model::Plot_unit_x::ePlot_unit_x::D_A);
|
|
break;
|
|
case MultiLinePlotUnits::Grid_um:
|
|
unit.setValue(org::openapitools::server::model::Plot_unit_x::ePlot_unit_x::GRID_UM);
|
|
break;
|
|
default:
|
|
break;
|
|
}
|
|
output.setUnitX(unit);
|
|
|
|
if (input.GetSizeX().has_value())
|
|
output.setSizeX(input.GetSizeX().value());
|
|
|
|
if (input.GetSizeY().has_value())
|
|
output.setSizeY(input.GetSizeY().value());
|
|
|
|
return output;
|
|
}
|
|
|
|
AzimuthalIntegrationSettings Convert(const org::openapitools::server::model::Azim_int_settings& input) {
|
|
AzimuthalIntegrationSettings ret{};
|
|
ret.SolidAngleCorrection(input.isSolidAngleCorr());
|
|
ret.PolarizationCorrection(input.isPolarizationCorr());
|
|
ret.QSpacing_recipA(input.getQSpacing());
|
|
ret.QRange_recipA(input.getLowQRecipA(),
|
|
input.highQRecipAIsSet() ? std::optional<float>(input.getHighQRecipA())
|
|
: std::nullopt);
|
|
ret.AzimuthalBinCount(input.getAzimuthalBins());
|
|
ret.ForceCPUinFPGAWorkflow(input.isForceCpu());
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Azim_int_settings Convert(const AzimuthalIntegrationSettings& settings) {
|
|
org::openapitools::server::model::Azim_int_settings ret{};
|
|
ret.setSolidAngleCorr(settings.IsSolidAngleCorrection());
|
|
ret.setPolarizationCorr(settings.IsPolarizationCorrection());
|
|
if (const auto high_q = settings.GetRequestedHighQ_recipA())
|
|
ret.setHighQRecipA(high_q.value());
|
|
ret.setLowQRecipA(settings.GetLowQ_recipA());
|
|
ret.setQSpacing(settings.GetQSpacing_recipA());
|
|
ret.setAzimuthalBins(settings.GetAzimuthalBinCount());
|
|
ret.setForceCpu(settings.IsForceCPUinFPGAWorkflow());
|
|
return ret;
|
|
}
|
|
|
|
ROIDefinition Convert(const org::openapitools::server::model::Roi_definitions& input) {
|
|
ROIDefinition output{};
|
|
for (const auto &i: input.getBox().getRois())
|
|
output.boxes.emplace_back(ROIBox(i.getName(), i.getMinXPxl(), i.getMaxXPxl(), i.getMinYPxl(), i.getMaxYPxl()));
|
|
for (const auto &i: input.getCircle().getRois())
|
|
output.circles.emplace_back(ROICircle(i.getName(), i.getCenterXPxl(), i.getCenterYPxl(), i.getRadiusPxl()));
|
|
for (const auto &i: input.getAzim().getRois()) {
|
|
// A sector needs both bounds; if only one is given, treat it as a full ring.
|
|
float phi_min = 0, phi_max = 0;
|
|
if (i.phiMinDegIsSet() && i.phiMaxDegIsSet()) {
|
|
phi_min = i.getPhiMinDeg();
|
|
phi_max = i.getPhiMaxDeg();
|
|
}
|
|
output.azimuthal.emplace_back(ROIAzimuthal(i.getName(),
|
|
(i.getQMaxRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMaxRecipA(),
|
|
(i.getQMinRecipA() == 0.0) ? 0.0 : 2.0f * PI / i.getQMinRecipA(),
|
|
phi_min, phi_max));
|
|
}
|
|
return output;
|
|
}
|
|
|
|
org::openapitools::server::model::Roi_circle_list Convert(const std::vector<ROICircle> &input) {
|
|
org::openapitools::server::model::Roi_circle_list ret{};
|
|
std::vector<org::openapitools::server::model::Roi_circle> tmp;
|
|
for (const auto &i: input) {
|
|
org::openapitools::server::model::Roi_circle elem;
|
|
elem.setName(i.GetName());
|
|
elem.setCenterXPxl(i.GetX());
|
|
elem.setCenterYPxl(i.GetY());
|
|
elem.setRadiusPxl(i.GetRadius_pxl());
|
|
tmp.emplace_back(elem);
|
|
}
|
|
ret.setRois(tmp);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Roi_azim_list Convert(const std::vector<ROIAzimuthal> &input) {
|
|
org::openapitools::server::model::Roi_azim_list ret{};
|
|
std::vector<org::openapitools::server::model::Roi_azimuthal> tmp;
|
|
for (const auto &i: input) {
|
|
org::openapitools::server::model::Roi_azimuthal elem;
|
|
elem.setName(i.GetName());
|
|
elem.setQMinRecipA(i.GetQMin_recipA());
|
|
elem.setQMaxRecipA(i.GetQMax_recipA());
|
|
if (i.HasPhi()) {
|
|
elem.setPhiMinDeg(i.GetPhiMin_deg());
|
|
elem.setPhiMaxDeg(i.GetPhiMax_deg());
|
|
}
|
|
tmp.emplace_back(elem);
|
|
}
|
|
ret.setRois(tmp);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Roi_box_list Convert(const std::vector<ROIBox> &input) {
|
|
org::openapitools::server::model::Roi_box_list ret{};
|
|
std::vector<org::openapitools::server::model::Roi_box> tmp;
|
|
for (const auto &i: input) {
|
|
org::openapitools::server::model::Roi_box elem;
|
|
elem.setName(i.GetName());
|
|
elem.setMinXPxl(i.GetXMin());
|
|
elem.setMaxXPxl(i.GetXMax());
|
|
elem.setMinYPxl(i.GetYMin());
|
|
elem.setMaxYPxl(i.GetYMax());
|
|
tmp.emplace_back(elem);
|
|
}
|
|
ret.setRois(tmp);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Roi_definitions Convert(const ROIDefinition &input) {
|
|
org::openapitools::server::model::Roi_definitions ret{};
|
|
ret.setCircle(Convert(input.circles));
|
|
ret.setBox(Convert(input.boxes));
|
|
ret.setAzim(Convert(input.azimuthal));
|
|
return ret;
|
|
}
|
|
|
|
ImageFormatSettings Convert(const org::openapitools::server::model::Image_format_settings& input) {
|
|
ImageFormatSettings ret{};
|
|
ret.GeometryTransformed(input.isGeometryTransform());
|
|
ret.AutoSummation(input.isSummation());
|
|
ret.JungfrauConversion(input.isJungfrauConversion());
|
|
ret.MaskChipEdges(input.isMaskChipEdges());
|
|
ret.MaskModuleEdges(input.isMaskModuleEdges());
|
|
ret.ApplyPixelMask(input.isApplyMask());
|
|
ret.PedestalG0RMSLimit(input.getJungfrauPedestalG0RmsLimit());
|
|
ret.MaskPixelsWithoutG0(input.isJungfrauMaskPixelsWithoutG0());
|
|
if (input.signedOutputIsSet())
|
|
ret.PixelSigned(input.isSignedOutput());
|
|
if (input.jungfrauConversionFactorKeVIsSet())
|
|
ret.JungfrauConvFactor_keV(input.getJungfrauConversionFactorKeV());
|
|
if (input.bitDepthImageIsSet())
|
|
ret.BitDepthImage(input.getBitDepthImage());
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Image_format_settings Convert(const ImageFormatSettings& input) {
|
|
org::openapitools::server::model::Image_format_settings ret{};
|
|
ret.setGeometryTransform(input.IsGeometryTransformed());
|
|
ret.setSummation(input.IsAutoSummation());
|
|
ret.setJungfrauConversion(input.IsJungfrauConversion());
|
|
ret.setMaskChipEdges(input.IsMaskChipEdges());
|
|
ret.setMaskModuleEdges(input.IsMaskModuleEdges());
|
|
ret.setApplyMask(input.IsApplyPixelMask());
|
|
ret.setJungfrauMaskPixelsWithoutG0(input.IsMaskPixelsWithoutG0());
|
|
ret.setJungfrauPedestalG0RmsLimit(input.GetPedestalG0RMSLimit());
|
|
if (input.IsPixelSigned().has_value())
|
|
ret.setSignedOutput(input.IsPixelSigned().value());
|
|
if (input.GetJungfrauConvFactor_keV().has_value())
|
|
ret.setJungfrauConversionFactorKeV(input.GetJungfrauConvFactor_keV().value());
|
|
if (input.GetBitDepthImage().has_value())
|
|
ret.setBitDepthImage(input.GetBitDepthImage().value());
|
|
return ret;
|
|
}
|
|
|
|
Coord ConvertOpenAPI(const std::vector<float> &input) {
|
|
if (input.size() != 3)
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Wrong size of Coord array");
|
|
return {input[0], input[1], input[2]};
|
|
}
|
|
|
|
GoniometerAxis Convert(const org::openapitools::server::model::Rotation_axis& input) {
|
|
std::optional<Coord> helical;
|
|
if (input.helicalStepUmIsSet())
|
|
helical = ConvertOpenAPI(input.getHelicalStepUm());
|
|
|
|
GoniometerAxis axis{input.getName(), input.getStart(), input.getStep(),
|
|
ConvertOpenAPI(input.getVector()), helical};
|
|
if (input.screeningWedgeDegIsSet())
|
|
axis.ScreeningWedge(input.getScreeningWedgeDeg());
|
|
return axis;
|
|
}
|
|
|
|
GridScanSettings Convert(const org::openapitools::server::model::Grid_scan& input) {
|
|
return {input.getNFast(), input.getStepXUm(), input.getStepYUm(), input.isSnake(), input.isVertical()};
|
|
}
|
|
|
|
DatasetSettings Convert(const org::openapitools::server::model::Dataset_settings& input) {
|
|
DatasetSettings ret;
|
|
|
|
ret.ImagesPerTrigger(input.getImagesPerTrigger());
|
|
ret.NumTriggers(input.getNtrigger());
|
|
|
|
if (input.runNumberIsSet())
|
|
ret.RunNumber(input.getRunNumber());
|
|
if (input.runNameIsSet())
|
|
ret.RunName(input.getRunName());
|
|
|
|
ret.ExperimentGroup(input.getExperimentGroup());
|
|
|
|
if (input.imageTimeUsIsSet())
|
|
ret.ImageTime(std::chrono::microseconds(input.getImageTimeUs()));
|
|
ret.BeamX_pxl(input.getBeamXPxl());
|
|
ret.BeamY_pxl(input.getBeamYPxl());
|
|
ret.DetectorDistance_mm(input.getDetectorDistanceMm());
|
|
ret.PhotonEnergy_keV(input.getIncidentEnergyKeV());
|
|
|
|
ret.FilePrefix(input.getFilePrefix());
|
|
|
|
if (!input.compressionIsSet())
|
|
ret.Compression(CompressionAlgorithm::BSHUF_LZ4);
|
|
else {
|
|
std::string compr = str_tolower(input.getCompression());
|
|
if (compr == "bslz4")
|
|
ret.Compression(CompressionAlgorithm::BSHUF_LZ4);
|
|
else if (compr == "bszstd")
|
|
ret.Compression(CompressionAlgorithm::BSHUF_ZSTD);
|
|
else if (compr == "bszstd_rle")
|
|
ret.Compression(CompressionAlgorithm::BSHUF_ZSTD_RLE);
|
|
else if (compr == "bszstd_rlehuf")
|
|
ret.Compression(CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF);
|
|
else if (compr == "none")
|
|
ret.Compression(CompressionAlgorithm::NO_COMPRESSION);
|
|
else
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown compression");
|
|
}
|
|
if (input.poissonCompressionIsSet())
|
|
ret.LossyCompressionPoisson(input.getPoissonCompression());
|
|
|
|
if (input.unitCellIsSet())
|
|
ret.SetUnitCell(UnitCell{
|
|
.a = input.getUnitCell().getA(),
|
|
.b = input.getUnitCell().getB(),
|
|
.c = input.getUnitCell().getC(),
|
|
.alpha = input.getUnitCell().getAlpha(),
|
|
.beta = input.getUnitCell().getBeta(),
|
|
.gamma = input.getUnitCell().getGamma()
|
|
});
|
|
|
|
if (input.totalFluxIsSet())
|
|
ret.TotalFlux(input.getTotalFlux());
|
|
if (input.beamSizeXUmIsSet())
|
|
ret.BeamSizeX_um(input.getBeamSizeXUm());
|
|
if (input.beamSizeYUmIsSet())
|
|
ret.BeamSizeY_um(input.getBeamSizeYUm());
|
|
if (input.transmissionIsSet())
|
|
ret.AttenuatorTransmission(input.getTransmission());
|
|
// Not alternatives: a grid scan is often collected at a given head position, so an axis and a
|
|
// grid can both be set. This used to drop the grid scan silently whenever an axis was present.
|
|
if (input.goniometerIsSet())
|
|
ret.Goniometer(Convert(input.getGoniometer()));
|
|
if (input.gridScanIsSet())
|
|
ret.GridScan(Convert(input.getGridScan()));
|
|
|
|
if (input.spaceGroupNumberIsSet())
|
|
ret.SpaceGroupNumber(input.getSpaceGroupNumber());
|
|
ret.SampleName(input.getSampleName());
|
|
ret.HeaderAppendix(input.getHeaderAppendix());
|
|
ret.ImageAppendix(input.getImageAppendix());
|
|
if (input.imagesPerFileIsSet())
|
|
ret.ImagesPerFile(input.getImagesPerFile());
|
|
|
|
if (input.dataReductionFactorSerialmxIsSet())
|
|
ret.LossyCompressionSerialMX(input.getDataReductionFactorSerialmx());
|
|
|
|
if (input.pixelValueLowThresholdIsSet())
|
|
ret.PixelValueLowThreshold(input.getPixelValueLowThreshold());
|
|
|
|
if (input.saveCalibrationIsSet())
|
|
ret.SaveCalibration(input.isSaveCalibration());
|
|
|
|
ret.WriteNXmxHDF5Master(input.isWriteNxmxHdf5Master());
|
|
|
|
if (input.polarizationFactorIsSet())
|
|
ret.PolarizationFactor(input.getPolarizationFactor());
|
|
|
|
ret.PoniRot1_rad(input.getPoniRot1Rad());
|
|
ret.PoniRot2_rad(input.getPoniRot2Rad());
|
|
ret.PoniRot3_rad(input.getPoniRot3Rad());
|
|
|
|
if (input.ringCurrentMAIsSet())
|
|
ret.RingCurrent_mA(input.getRingCurrentMA());
|
|
if (input.sampleTemperatureKIsSet())
|
|
ret.SampleTemperature_K(input.getSampleTemperatureK());
|
|
|
|
ret.SpotFindingEnable(input.isSpotFinding());
|
|
ret.MaxSpotCount(input.getMaxSpotCount());
|
|
|
|
ret.DetectIceRings(input.isDetectIceRings());
|
|
|
|
if (input.xrayFluorescenceSpectrumIsSet()) {
|
|
auto fl = input.getXrayFluorescenceSpectrum();
|
|
ret.FluorescenceSpectrum({fl.getEnergyEV(), fl.getData()});
|
|
}
|
|
|
|
if (input.smargonIsSet()) {
|
|
auto sm = input.getSmargon();
|
|
SmargonPosition smargon;
|
|
smargon.phi_deg = sm.getPhiDeg();
|
|
smargon.chi_deg = sm.getChiDeg();
|
|
if (sm.phiAxisIsSet())
|
|
smargon.phi_axis = ConvertOpenAPI(sm.getPhiAxis());
|
|
if (sm.chiAxisIsSet())
|
|
smargon.chi_axis = ConvertOpenAPI(sm.getChiAxis());
|
|
ret.Smargon(smargon);
|
|
}
|
|
|
|
return ret;
|
|
}
|
|
|
|
std::vector<org::openapitools::server::model::Fpga_status_inner> Convert(const std::vector<DeviceStatus> &input) {
|
|
std::vector<org::openapitools::server::model::Fpga_status_inner> ret;
|
|
for (const auto &d: input) {
|
|
org::openapitools::server::model::Fpga_status_inner tmp;
|
|
tmp.setPciDevId(d.device_number);
|
|
tmp.setSerialNumber(d.serial_number);
|
|
tmp.setFwVersion(d.fpga_firmware_version);
|
|
tmp.setBaseMacAddr(MacAddressToStr(d.fpga_default_mac_addr));
|
|
tmp.setPacketsSls(d.packets_sls);
|
|
tmp.setPacketsUdp(d.packets_udp);
|
|
tmp.setEthLinkCount(d.eth_link_count);
|
|
tmp.setEthLinkStatus(d.eth_link_status);
|
|
tmp.setFpgaTempC(static_cast<float>(d.fpga_temp_C));
|
|
tmp.setHbmTempC(static_cast<float>(d.hbm_0_temp_C));
|
|
tmp.setPowerUsageW(static_cast<float>(d.fpga_pcie_12V_I_mA * d.fpga_pcie_12V_V_mV + d.fpga_pcie_3p3V_I_mA
|
|
* d.fpga_pcie_3p3V_V_mV) / (1000.0f * 1000.0f));
|
|
tmp.setIdle(d.idle);
|
|
tmp.setPcieLinkSpeed(d.pcie_link_speed);
|
|
tmp.setPcieLinkWidth(d.pcie_link_width);
|
|
ret.emplace_back(std::move(tmp));
|
|
}
|
|
return ret;
|
|
}
|
|
|
|
ZMQPreviewSettings Convert(const org::openapitools::server::model::Zeromq_preview_settings &input) {
|
|
ZMQPreviewSettings ret;
|
|
if (input.isEnabled())
|
|
ret.period = std::chrono::milliseconds(input.getPeriodMs());
|
|
else
|
|
ret.period = {};
|
|
ret.address = "";
|
|
return ret;
|
|
}
|
|
|
|
ZMQMetadataSettings Convert(const org::openapitools::server::model::Zeromq_metadata_settings &input) {
|
|
ZMQMetadataSettings ret;
|
|
if (input.isEnabled())
|
|
ret.period = std::chrono::milliseconds(input.getPeriodMs());
|
|
else
|
|
ret.period = {};
|
|
ret.address = "";
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Zeromq_preview_settings Convert(const ZMQPreviewSettings &settings) {
|
|
org::openapitools::server::model::Zeromq_preview_settings ret;
|
|
ret.setEnabled(settings.period.has_value());
|
|
if (settings.period.has_value())
|
|
ret.setPeriodMs(std::chrono::round<std::chrono::milliseconds>(settings.period.value()).count());
|
|
ret.setSocketAddress(settings.address);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Zeromq_metadata_settings Convert(const ZMQMetadataSettings &settings) {
|
|
org::openapitools::server::model::Zeromq_metadata_settings ret;
|
|
ret.setEnabled(settings.period.has_value());
|
|
if (settings.period.has_value())
|
|
ret.setPeriodMs(std::chrono::round<std::chrono::milliseconds>(settings.period.value()).count());
|
|
ret.setSocketAddress(settings.address);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Pixel_mask_statistics Convert(const PixelMaskStatistics& input) {
|
|
org::openapitools::server::model::Pixel_mask_statistics ret;
|
|
ret.setUserMask(input.user_mask);
|
|
ret.setWrongGain(input.error_pixel);
|
|
ret.setTooHighPedestalRms(input.noisy_pixel);
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Image_buffer_status Convert(const ImageBufferStatus& input) {
|
|
org::openapitools::server::model::Image_buffer_status ret;
|
|
ret.setAvailableSlots(input.available_slots);
|
|
ret.setTotalSlots(input.total_slots);
|
|
ret.setImageNumbers(input.images_in_the_buffer);
|
|
ret.setMaxImageNumber(input.max_image_number);
|
|
ret.setMinImageNumber(input.min_image_number);
|
|
ret.setInPreparationSlots(input.preparation_slots);
|
|
ret.setInSendingSlots(input.sending_slots);
|
|
|
|
if (input.current_counter.has_value())
|
|
ret.setCurrentCounter(input.current_counter.value());
|
|
return ret;
|
|
}
|
|
|
|
ImageBufferStatus Convert(const org::openapitools::server::model::Image_buffer_status& input) {
|
|
ImageBufferStatus ret;
|
|
ret.available_slots = input.getAvailableSlots();
|
|
ret.total_slots = input.getTotalSlots();
|
|
ret.images_in_the_buffer = input.getImageNumbers();
|
|
ret.max_image_number = input.getMaxImageNumber();
|
|
ret.min_image_number = input.getMinImageNumber();
|
|
ret.sending_slots = input.getInSendingSlots();
|
|
ret.preparation_slots = input.getInPreparationSlots();
|
|
|
|
if (input.currentCounterIsSet())
|
|
ret.current_counter = input.getCurrentCounter();
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::File_writer_settings Convert(const FileWriterSettings& input) {
|
|
org::openapitools::server::model::File_writer_settings ret;
|
|
ret.setFormat(Convert(input.GetFileFormat()));
|
|
ret.setOverwrite(input.IsOverwriteExistingFiles());
|
|
return ret;
|
|
}
|
|
|
|
FileWriterSettings Convert(const org::openapitools::server::model::File_writer_settings &input) {
|
|
FileWriterSettings ret;
|
|
ret.OverwriteExistingFiles(input.isOverwrite());
|
|
ret.FileFormat(Convert(input.getFormat()));
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::File_writer_format Convert(FileWriterFormat input) {
|
|
org::openapitools::server::model::File_writer_format ret;
|
|
switch (input) {
|
|
case FileWriterFormat::DataOnly:
|
|
ret.setValue(org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXONLYDATA);
|
|
break;
|
|
case FileWriterFormat::NXmxLegacy:
|
|
ret.setValue(org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXLEGACY);
|
|
break;
|
|
case FileWriterFormat::NXmxVDS:
|
|
ret.setValue(org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXVDS);
|
|
break;
|
|
case FileWriterFormat::NXmxIntegrated:
|
|
ret.setValue(org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXINTEGRATED);
|
|
break;
|
|
case FileWriterFormat::NoFile:
|
|
ret.setValue(org::openapitools::server::model::File_writer_format::eFile_writer_format::NOFILEWRITTEN);
|
|
break;
|
|
default:
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown file writer format enum value");
|
|
}
|
|
return ret;
|
|
}
|
|
|
|
FileWriterFormat Convert(const org::openapitools::server::model::File_writer_format& input) {
|
|
switch (input.getValue()) {
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXONLYDATA:
|
|
return FileWriterFormat::DataOnly;
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXLEGACY:
|
|
return FileWriterFormat::NXmxLegacy;
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXVDS:
|
|
return FileWriterFormat::NXmxVDS;
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::NXMXINTEGRATED:
|
|
return FileWriterFormat::NXmxIntegrated;
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::CBF:
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::TIFF:
|
|
// Deprecated, kept in the OpenAPI enum for back compatibility only - only HDF5 is written now.
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"CBF and TIFF file formats are no longer supported");
|
|
case org::openapitools::server::model::File_writer_format::eFile_writer_format::NOFILEWRITTEN:
|
|
return FileWriterFormat::NoFile;
|
|
default:
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Unknown file writer format enum value");
|
|
}
|
|
}
|
|
|
|
PlotType ConvertPlotType(const std::optional<std::string>& input) {
|
|
if (!input.has_value())
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Plot type is compulsory paramater");
|
|
if (input == "bkg_estimate") return PlotType::BkgEstimate;
|
|
if (input == "spindle_blind_fraction") return PlotType::SpindleBlindFraction;
|
|
if (input == "ice_ring_score") return PlotType::IceRingScore;
|
|
if (input == "azint") return PlotType::AzInt;
|
|
if (input == "azint_1d") return PlotType::AzInt1D;
|
|
if (input == "spot_count") return PlotType::SpotCount;
|
|
if (input == "spot_count_low_res") return PlotType::SpotCountLowRes;
|
|
if (input == "spot_count_indexed") return PlotType::SpotCountIndexed;
|
|
if (input == "spot_count_ice") return PlotType::SpotCountIceRing;
|
|
if (input == "indexing_rate") return PlotType::IndexingRate;
|
|
if (input == "indexing_unit_cell_length") return PlotType::IndexingUnitCellLength;
|
|
if (input == "profile_radius") return PlotType::ProfileRadius;
|
|
if (input == "mosaicity") return PlotType::Mosaicity;
|
|
if (input == "b_factor") return PlotType::BFactor;
|
|
if (input == "indexing_unit_cell_angle") return PlotType::IndexingUnitCellAngle;
|
|
if (input == "error_pixels") return PlotType::ErrorPixels;
|
|
if (input == "strong_pixels") return PlotType::StrongPixels;
|
|
if (input == "saturated_pixels") return PlotType::SaturatedPixels;
|
|
if (input == "image_collection_efficiency") return PlotType::ImageCollectionEfficiency;
|
|
if (input == "receiver_delay") return PlotType::ReceiverDelay;
|
|
if (input == "receiver_free_send_buf") return PlotType::ReceiverFreeSendBuf;
|
|
if (input == "roi_sum") return PlotType::ROISum;
|
|
if (input == "roi_mean") return PlotType::ROIMean;
|
|
if (input == "roi_max_count") return PlotType::ROIMaxCount;
|
|
if (input == "roi_pixels") return PlotType::ROIPixels;
|
|
if (input == "roi_weighted_x") return PlotType::ROIWeightedX;
|
|
if (input == "roi_weighted_y") return PlotType::ROIWeightedY;
|
|
if (input == "packets_received") return PlotType::PacketsReceived;
|
|
if (input == "max_pixel_value") return PlotType::MaxValue;
|
|
if (input == "resolution_estimate") return PlotType::ResolutionEstimate;
|
|
if (input == "pixel_sum") return PlotType::PixelSum;
|
|
if (input == "processing_time") return PlotType::ImageProcessingTime;
|
|
if (input == "beam_center_x") return PlotType::RefinementBeamX;
|
|
if (input == "beam_center_y") return PlotType::RefinementBeamY;
|
|
if (input == "integrated_reflections") return PlotType::IntegratedReflections;
|
|
if (input == "image_scale_factor") return PlotType::ImageScaleFactor;
|
|
if (input == "image_scale_cc") return PlotType::ImageScaleCC;
|
|
if (input == "compression_ratio") return PlotType::CompressionRatio;
|
|
if (input == "indexing_lattice_count") return PlotType::IndexingLatticeCount;
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Plot type not recognized");
|
|
}
|
|
|
|
ColorScaleEnum ConvertColorScale(const std::optional<std::string> &input) {
|
|
std::string color = input.value_or("indigo");
|
|
|
|
if (color == "viridis")
|
|
return ColorScaleEnum::Viridis;
|
|
if (color == "bw")
|
|
return ColorScaleEnum::BW;
|
|
if (color == "wb")
|
|
return ColorScaleEnum::WB;
|
|
if (color == "green")
|
|
return ColorScaleEnum::Green;
|
|
if (color == "heat")
|
|
return ColorScaleEnum::Heat;
|
|
if (color == "indigo")
|
|
return ColorScaleEnum::Indigo;
|
|
if (color == "magma")
|
|
return ColorScaleEnum::Magma;
|
|
if (color == "inferno")
|
|
return ColorScaleEnum::Inferno;
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Color scale unknown");
|
|
}
|
|
|
|
IndexingSettings Convert(const org::openapitools::server::model::Indexing_settings &input) {
|
|
IndexingSettings ret;
|
|
switch (input.getAlgorithm().getValue()) {
|
|
case org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::FFT:
|
|
ret.Algorithm(IndexingAlgorithmEnum::FFT);
|
|
break;
|
|
case org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::FFTW:
|
|
ret.Algorithm(IndexingAlgorithmEnum::FFTW);
|
|
break;
|
|
case org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::NONE:
|
|
ret.Algorithm(IndexingAlgorithmEnum::None);
|
|
break;
|
|
case org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::FFBIDX:
|
|
ret.Algorithm(IndexingAlgorithmEnum::FFBIDX);
|
|
break;
|
|
case org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::AUTO:
|
|
ret.Algorithm(IndexingAlgorithmEnum::Auto);
|
|
break;
|
|
default:
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown indexing algorithm");
|
|
}
|
|
|
|
switch (input.getGeomRefinementAlgorithm().getValue()) {
|
|
case org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::INVALID_VALUE_OPENAPI_GENERATED:
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown refinement algorithm");
|
|
break;
|
|
case org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::BEAMCENTER:
|
|
ret.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
|
|
break;
|
|
case org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::ORIENTATIONONLY:
|
|
ret.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::OrientationOnly);
|
|
break;
|
|
case org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::FLEX:
|
|
ret.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::Flex);
|
|
break;
|
|
case org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::NONE:
|
|
ret.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::None);
|
|
break;
|
|
}
|
|
|
|
ret.FFT_HighResolution_A(input.getFftHighResolutionA());
|
|
ret.FFT_MaxUnitCell_A(input.getFftMaxUnitCellA());
|
|
ret.FFT_MinUnitCell_A(input.getFftMinUnitCellA());
|
|
ret.FFT_NumVectors(input.getFftNumVectors());
|
|
ret.Tolerance(input.getTolerance());
|
|
ret.IndexingThreads(input.getThreadCount());
|
|
ret.UnitCellDistTolerance(input.getUnitCellDistTolerance());
|
|
ret.ViableCellMinSpots(input.getViableCellMinSpots());
|
|
ret.IndexIceRings(input.isIndexIceRings());
|
|
ret.RotationIndexing(input.isRotationIndexing());
|
|
ret.RotationIndexingAngularStride_deg(input.getRotationIndexingAngularStrideDeg());
|
|
ret.RotationIndexingMinAngularRange_deg(input.getRotationIndexingMinAngularRangeDeg());
|
|
ret.BlockingBehavior(input.isBlocking());
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Indexing_settings Convert(const IndexingSettings &input) {
|
|
org::openapitools::server::model::Indexing_settings ret;
|
|
|
|
ret.setFftHighResolutionA(input.GetFFT_HighResolution_A());
|
|
ret.setFftMinUnitCellA(input.GetFFT_MinUnitCell_A());
|
|
ret.setFftMaxUnitCellA(input.GetFFT_MaxUnitCell_A());
|
|
ret.setFftNumVectors(input.GetFFT_NumVectors());
|
|
ret.setTolerance(input.GetTolerance());
|
|
ret.setThreadCount(input.GetIndexingThreads());
|
|
ret.setUnitCellDistTolerance(input.GetUnitCellDistTolerance());
|
|
ret.setViableCellMinSpots(input.GetViableCellMinSpots());
|
|
ret.setRotationIndexing(input.GetRotationIndexing());
|
|
ret.setRotationIndexingAngularStrideDeg(input.GetRotationIndexingAngularStride_deg());
|
|
ret.setRotationIndexingMinAngularRangeDeg(input.GetRotationIndexingMinAngularRange_deg());
|
|
ret.setBlocking(input.GetBlockingBehavior());
|
|
|
|
org::openapitools::server::model::Geom_refinement_algorithm refinement;
|
|
switch (input.GetGeomRefinementAlgorithm()) {
|
|
|
|
case GeomRefinementAlgorithmEnum::None:
|
|
refinement.setValue(org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::NONE);
|
|
break;
|
|
case GeomRefinementAlgorithmEnum::BeamCenter:
|
|
refinement.setValue(org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::BEAMCENTER);
|
|
break;
|
|
case GeomRefinementAlgorithmEnum::OrientationOnly:
|
|
refinement.setValue(org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::ORIENTATIONONLY);
|
|
break;
|
|
case GeomRefinementAlgorithmEnum::Flex:
|
|
refinement.setValue(org::openapitools::server::model::Geom_refinement_algorithm::eGeom_refinement_algorithm::FLEX);
|
|
break;
|
|
}
|
|
|
|
ret.setGeomRefinementAlgorithm(refinement);
|
|
|
|
org::openapitools::server::model::Indexing_algorithm tmp;
|
|
switch (input.GetAlgorithm()) {
|
|
case IndexingAlgorithmEnum::Auto:
|
|
tmp.setValue(org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::AUTO);
|
|
break;
|
|
case IndexingAlgorithmEnum::FFBIDX:
|
|
tmp.setValue(org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::FFBIDX);
|
|
break;
|
|
case IndexingAlgorithmEnum::FFT:
|
|
tmp.setValue(org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::FFT);
|
|
break;
|
|
case IndexingAlgorithmEnum::FFTW:
|
|
tmp.setValue(org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::FFTW);
|
|
break;
|
|
case IndexingAlgorithmEnum::None:
|
|
tmp.setValue(org::openapitools::server::model::Indexing_algorithm::eIndexing_algorithm::NONE);
|
|
break;
|
|
}
|
|
ret.setAlgorithm(tmp);
|
|
ret.setIndexIceRings(input.GetIndexIceRings());
|
|
return ret;
|
|
}
|
|
|
|
BraggIntegrationSettings Convert(const org::openapitools::server::model::Bragg_integration_settings &input) {
|
|
BraggIntegrationSettings ret;
|
|
switch (input.getIntegrationModel().getValue()) {
|
|
case org::openapitools::server::model::Integration_model::eIntegration_model::PROFILEGAUSSIAN:
|
|
ret.Integrator(IntegratorMode::ProfileGaussian);
|
|
break;
|
|
case org::openapitools::server::model::Integration_model::eIntegration_model::PROFILEEMPIRICAL:
|
|
ret.Integrator(IntegratorMode::ProfileEmpirical);
|
|
break;
|
|
case org::openapitools::server::model::Integration_model::eIntegration_model::BOXSUM:
|
|
ret.Integrator(IntegratorMode::BoxSum);
|
|
break;
|
|
default:
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown integration model");
|
|
}
|
|
// Always a concrete number online, never "derive it from the crystal": the generated model holds
|
|
// the schema's default when the request omits the field, so an absent max_hkl arrives here as that
|
|
// default rather than as an absent value. Deriving per crystal would make a live acquisition's
|
|
// per-image cost depend on whichever sample is mounted.
|
|
ret.MaxHKL(input.getMaxHkl());
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Bragg_integration_settings Convert(const BraggIntegrationSettings &input) {
|
|
org::openapitools::server::model::Bragg_integration_settings ret;
|
|
org::openapitools::server::model::Integration_model tmp;
|
|
switch (input.GetIntegrator()) {
|
|
case IntegratorMode::ProfileGaussian:
|
|
tmp.setValue(org::openapitools::server::model::Integration_model::eIntegration_model::PROFILEGAUSSIAN);
|
|
break;
|
|
case IntegratorMode::ProfileEmpirical:
|
|
tmp.setValue(org::openapitools::server::model::Integration_model::eIntegration_model::PROFILEEMPIRICAL);
|
|
break;
|
|
case IntegratorMode::BoxSum:
|
|
tmp.setValue(org::openapitools::server::model::Integration_model::eIntegration_model::BOXSUM);
|
|
break;
|
|
}
|
|
ret.setIntegrationModel(tmp);
|
|
if (const auto max_hkl = input.GetMaxHKL())
|
|
ret.setMaxHkl(*max_hkl);
|
|
return ret;
|
|
}
|
|
|
|
AnalysisSettings Convert(const org::openapitools::server::model::Analysis_settings &input) {
|
|
AnalysisSettings ret;
|
|
// No default: the compiler must object here when a mode is added to the API, rather than let the
|
|
// new value fall through to whatever the last branch was. MXRotation is not in the API at all -
|
|
// jfjoch_broker has no rotation analysis path - so there is no case for it.
|
|
switch (input.getMode().getValue()) {
|
|
case org::openapitools::server::model::Analysis_mode::eAnalysis_mode::INVALID_VALUE_OPENAPI_GENERATED:
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Unknown analysis mode");
|
|
case org::openapitools::server::model::Analysis_mode::eAnalysis_mode::NONE:
|
|
ret.Mode(AnalysisMode::None);
|
|
break;
|
|
case org::openapitools::server::model::Analysis_mode::eAnalysis_mode::MXSTILLS:
|
|
ret.Mode(AnalysisMode::MXStills);
|
|
break;
|
|
case org::openapitools::server::model::Analysis_mode::eAnalysis_mode::AZINT:
|
|
ret.Mode(AnalysisMode::Azint);
|
|
break;
|
|
case org::openapitools::server::model::Analysis_mode::eAnalysis_mode::GRID:
|
|
ret.Mode(AnalysisMode::Grid);
|
|
break;
|
|
case org::openapitools::server::model::Analysis_mode::eAnalysis_mode::POWDERCALIBRATION:
|
|
ret.Mode(AnalysisMode::PowderCalibration);
|
|
break;
|
|
}
|
|
|
|
if (input.calibrantIsSet())
|
|
ret.Calibrant(input.getCalibrant());
|
|
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Analysis_settings Convert(const AnalysisSettings &input) {
|
|
org::openapitools::server::model::Analysis_settings ret;
|
|
org::openapitools::server::model::Analysis_mode tmp;
|
|
switch (input.GetMode()) {
|
|
case AnalysisMode::None:
|
|
tmp.setValue(org::openapitools::server::model::Analysis_mode::eAnalysis_mode::NONE);
|
|
break;
|
|
case AnalysisMode::MXStills:
|
|
tmp.setValue(org::openapitools::server::model::Analysis_mode::eAnalysis_mode::MXSTILLS);
|
|
break;
|
|
case AnalysisMode::Azint:
|
|
tmp.setValue(org::openapitools::server::model::Analysis_mode::eAnalysis_mode::AZINT);
|
|
break;
|
|
case AnalysisMode::Grid:
|
|
tmp.setValue(org::openapitools::server::model::Analysis_mode::eAnalysis_mode::GRID);
|
|
break;
|
|
case AnalysisMode::PowderCalibration:
|
|
tmp.setValue(org::openapitools::server::model::Analysis_mode::eAnalysis_mode::POWDERCALIBRATION);
|
|
break;
|
|
case AnalysisMode::MXRotation:
|
|
// Unreachable through the API: the setter refuses it, so it can never be stored. Reported
|
|
// rather than silently rewritten to stills, which would be the broker claiming to run an
|
|
// analysis it does not have.
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Rotation MX analysis cannot be reported by this API");
|
|
}
|
|
ret.setMode(tmp);
|
|
if (!input.GetCalibrant().empty())
|
|
ret.setCalibrant(input.GetCalibrant());
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Scan_result Convert(const ScanResult& input) {
|
|
org::openapitools::server::model::Scan_result ret;
|
|
ret.setFilePrefix(input.file_prefix);
|
|
std::vector<org::openapitools::server::model::Scan_result_images_inner> v;
|
|
for (const auto &i : input.images) {
|
|
org::openapitools::server::model::Scan_result_images_inner tmp;
|
|
tmp.setEfficiency(i.collection_efficiency);
|
|
tmp.setNumber(i.number);
|
|
if (i.x.has_value())
|
|
tmp.setNx(i.x.value());
|
|
if (i.y.has_value())
|
|
tmp.setNy(i.y.value());
|
|
|
|
if (i.bkg.has_value())
|
|
tmp.setBkg(i.bkg.value());
|
|
if (i.spindle_blind.has_value())
|
|
tmp.setSpindleBlind(i.spindle_blind.value());
|
|
|
|
if (i.angle_deg.has_value())
|
|
tmp.setAngle(i.angle_deg.value());
|
|
if (i.pixel_sum.has_value())
|
|
tmp.setPixelSum(i.pixel_sum.value());
|
|
if (i.max_viable_pixel.has_value())
|
|
tmp.setMax(i.max_viable_pixel.value());
|
|
if (i.sat_pixels.has_value())
|
|
tmp.setSat(i.sat_pixels.value());
|
|
if (i.spot_count.has_value())
|
|
tmp.setSpots(i.spot_count.value());
|
|
if (i.spot_count_ice.has_value())
|
|
tmp.setSpotsIce(i.spot_count_ice.value());
|
|
if (i.ice_ring_score.has_value())
|
|
tmp.setIce(i.ice_ring_score.value());
|
|
if (i.spot_count_low_res.has_value())
|
|
tmp.setSpotsLowRes(i.spot_count_low_res.value());
|
|
if (i.spot_count_indexed.has_value())
|
|
tmp.setSpotsIndexed(i.spot_count_indexed.value());
|
|
if (i.indexing_solution.has_value())
|
|
tmp.setIndex(i.indexing_solution.value());
|
|
if (i.profile_radius.has_value())
|
|
tmp.setPr(i.profile_radius.value());
|
|
if (i.b_factor.has_value())
|
|
tmp.setB(i.b_factor.value());
|
|
if (i.uc.has_value()) {
|
|
org::openapitools::server::model::Unit_cell uc;
|
|
uc.setA(i.uc->a);
|
|
uc.setB(i.uc->b);
|
|
uc.setC(i.uc->c);
|
|
uc.setAlpha(i.uc->alpha);
|
|
uc.setBeta(i.uc->beta);
|
|
uc.setGamma(i.uc->gamma);
|
|
tmp.setUc(uc);
|
|
}
|
|
if (i.indexed_lattice_count.has_value())
|
|
tmp.setLattCount(i.indexed_lattice_count.value());
|
|
if (i.xfel_pulse_id.has_value())
|
|
tmp.setXfelPulseid(i.xfel_pulse_id.value());
|
|
if (i.res.has_value())
|
|
tmp.setRes(i.res.value());
|
|
v.emplace_back(std::move(tmp));
|
|
}
|
|
ret.setImages(v);
|
|
if (input.rotation_lattice) {
|
|
ret.setRotationCrystalLattice(input.rotation_lattice->GetVector());
|
|
org::openapitools::server::model::Unit_cell uc;
|
|
auto i_uc = input.rotation_lattice->GetUnitCell();
|
|
|
|
uc.setA(i_uc.a);
|
|
uc.setB(i_uc.b);
|
|
uc.setC(i_uc.c);
|
|
uc.setAlpha(i_uc.alpha);
|
|
uc.setBeta(i_uc.beta);
|
|
uc.setGamma(i_uc.gamma);
|
|
ret.setRotationUnitCell(uc);
|
|
}
|
|
if (input.rotation_crystal_system && input.rotation_centering)
|
|
ret.setRotationBravais(BravaisSymbol(*input.rotation_crystal_system, *input.rotation_centering));
|
|
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Dark_mask_settings Convert(const DarkMaskSettings &input) {
|
|
org::openapitools::server::model::Dark_mask_settings ret{};
|
|
ret.setDetectorThresholdKeV(input.GetThreshold_keV());
|
|
ret.setFrameTimeUs(std::chrono::round<std::chrono::microseconds>(
|
|
std::chrono::duration<float>(input.GetFrameTime())
|
|
).count());
|
|
ret.setMaxFramesWithSignal(input.GetMaxFramesWithCounts());
|
|
ret.setMaxAllowedPixelCount(input.GetMaxCounts());
|
|
ret.setNumberOfFrames(input.GetNumberOfFrames());
|
|
return ret;
|
|
}
|
|
|
|
DarkMaskSettings Convert(const org::openapitools::server::model::Dark_mask_settings &input) {
|
|
DarkMaskSettings ret{};
|
|
ret.FrameTime(std::chrono::microseconds(input.getFrameTimeUs()))
|
|
.NumberOfFrames(input.getNumberOfFrames())
|
|
.MaxCounts(input.getMaxAllowedPixelCount())
|
|
.MaxFramesWithCounts(input.getMaxFramesWithSignal())
|
|
.Threshold_keV(input.getDetectorThresholdKeV());
|
|
return ret;
|
|
}
|
|
|
|
org::openapitools::server::model::Image_pusher_status Convert(const ImagePusherStatus& input) {
|
|
org::openapitools::server::model::Image_pusher_status ret;
|
|
ret.setAddr(input.address);
|
|
ret.setConnectedWriters(input.connected_writers);
|
|
org::openapitools::server::model::Image_pusher_type tmp;
|
|
switch (input.pusher_type) {
|
|
case ImagePusherType::HDF5:
|
|
tmp.setValue(org::openapitools::server::model::Image_pusher_type::eImage_pusher_type::HDF5);
|
|
break;
|
|
case ImagePusherType::CBOR:
|
|
tmp.setValue(org::openapitools::server::model::Image_pusher_type::eImage_pusher_type::CBOR);
|
|
break;
|
|
case ImagePusherType::TCP:
|
|
tmp.setValue(org::openapitools::server::model::Image_pusher_type::eImage_pusher_type::TCP);
|
|
break;
|
|
case ImagePusherType::ZMQ:
|
|
tmp.setValue(org::openapitools::server::model::Image_pusher_type::eImage_pusher_type::ZEROMQ);
|
|
break;
|
|
default:
|
|
tmp.setValue(org::openapitools::server::model::Image_pusher_type::eImage_pusher_type::NONE);
|
|
break;
|
|
}
|
|
ret.setPusherType(tmp);
|
|
if (input.images_written)
|
|
ret.setImagesWritten(input.images_written.value());
|
|
if (input.images_write_error)
|
|
ret.setImagesWriteError(input.images_write_error.value());
|
|
ret.setWriterFifoUtilization(input.writer_fifo_utilization);
|
|
return ret;
|
|
} |