leonarski_fandClaude Opus 5
26a82ddc72
The score was computed and then thrown away - carried on the per-image message but transported nowhere - so the automation it exists for could not read it. It now flows like bkg_estimate at every layer: CBOR (per-image key, END-block run mean and per-image array), HDF5 (per-image /entry/MX/spindleBlindFraction in the data files, the array and spindleBlindFractionMean in the master), read-back into a re-opened dataset, the scan result, the receiver plots, the REST plot and scan_result schemas, and the viewer and frontend plot menus. Absence is load-bearing and every transport keeps it distinguishable from a measured zero: the CBOR key is simply missing, the HDF5 array holds NaN, and read-back turns NaN back into an absent optional rather than a value. A pipeline that read 0 where the truth is "no value" would take exactly the wrong action - a measured 0 says one sweep loses nothing, absence says nobody could look, and the second must engage the recovery protocol while the first must not. The round-trip tests pin all three states through CBOR and through a written-and-reopened file. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
73 lines
2.5 KiB
C++
73 lines
2.5 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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#pragma once
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#include "HDF5DataFilePlugin.h"
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#include "../common/AutoIncrVector.h"
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class HDF5DataFilePluginMX : public HDF5DataFilePlugin {
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const size_t max_spots;
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const size_t max_extra_lattices;
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const bool indexing;
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// spots
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std::vector<float> spot_x;
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std::vector<float> spot_y;
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std::vector<float> spot_int;
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std::vector<int8_t> spot_indexed;
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std::vector<int8_t> spot_ice_ring;
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std::vector<int8_t> spot_lattice;
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std::vector<int32_t> spot_h;
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std::vector<int32_t> spot_k;
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std::vector<int32_t> spot_l;
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std::vector<float> spot_dist_ewald;
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AutoIncrVector<float> beam_corr_x{NAN};
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AutoIncrVector<float> beam_corr_y{NAN};
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AutoIncrVector<uint32_t> npeaks;
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AutoIncrVector<uint32_t> strong_pixel_count;
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AutoIncrVector<uint32_t> spot_count_total;
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AutoIncrVector<uint32_t> spot_count_ice;
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AutoIncrVector<float> spot_count_ice_control{NAN};
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AutoIncrVector<uint32_t> spot_count_indexed;
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AutoIncrVector<uint32_t> spot_count_low_res;
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// indexing
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AutoIncrVector<uint8_t> indexed;
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AutoIncrVector<uint32_t> indexing_lattice_count;
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std::vector<float> indexed_lattice;
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std::vector<float> extra_lattices; // [nimages, max_extra_lattices, 9], NaN-filled
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// crystal
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AutoIncrVector<float> profile_radius{NAN};
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AutoIncrVector<float> mosaicity_deg{NAN};
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AutoIncrVector<float> b_factor{NAN};
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// bkg_estimate
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AutoIncrVector<float> bkg_estimate{NAN};
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AutoIncrVector<float> ice_ring_score{NAN};
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// NaN = the frame had no value (CANNOT SAY), which is not a zero - see SpindleTrigger.
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AutoIncrVector<float> spindle_blind_fraction{NAN};
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// resolution_estimation
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AutoIncrVector<float> resolution_estimate{NAN};
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AutoIncrVector<uint32_t> niggli_class;
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AutoIncrVector<std::string> bravais_lattice;
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AutoIncrVector<int64_t> integrated_reflections;
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// scaling
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bool image_scale_present = false;
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AutoIncrVector<float> image_scale_factor{NAN};
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AutoIncrVector<float> image_scale_cc{NAN};
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AutoIncrVector<float> image_scale_mosaicity{NAN};
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public:
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explicit HDF5DataFilePluginMX(const StartMessage& msg);
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void OpenFile(HDF5File &data_file, const DataMessage& msg, size_t images_per_file) override;
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void Write(const DataMessage& msg, uint64_t image_number) override;
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void WriteFinal(HDF5File &data_file) override;
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};
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