leonarski_fandClaude Opus 5
14e2bf3c0f
Both lanes added a per-image scalar to the same eleven files, so every conflict was two
additions competing for one line. All were resolved by keeping both, with three that needed
more than that:
- ScanResultGenerator: rc167 changed the per-image float vectors to resize(n, NAN) so a frame
that never arrived does not read back as a real 0. v_protein_score and v_ice_score are exactly
that case - 0 is a real answer ("nothing detected here") - so they take the NAN default too.
- HDF5MetadataSource: rc167 established that NaN in a stored per-image array means "no value" and
the optional must come back absent. The two detection scores now follow it, which they did not
before the merge; without the guard a missing score would come back as a NaN that a threshold
would silently compare against.
- CBORTest: designated initialisers must follow member declaration order, so spindle_blind_fraction
precedes the two scores in the DataMessage aggregate.
Verified after the merge that every CBOR key that is encoded is also decoded (198 encoded keys,
one intentional exception: the "type" discriminator), that both lanes' fields survive in the
writer, the reader, the plots and the API, and that a stored file still round-trips.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
75 lines
2.6 KiB
C++
75 lines
2.6 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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AutoIncrVector<float> protein_score{NAN};
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AutoIncrVector<float> ice_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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