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
108 lines
4.6 KiB
C++
108 lines
4.6 KiB
C++
// SPDX-FileCopyrightText: 2025 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 <string>
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#include <array>
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#include <optional>
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#include <vector>
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#include <map>
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#include <memory>
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#include "../common/DiffractionGeometry.h"
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#include "../common/DiffractionExperiment.h"
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#include "../common/PixelMask.h"
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#include "../common/AzimuthalIntegrationMapping.h"
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struct JFJochReaderDataset {
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std::string arm_date;
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DiffractionExperiment experiment;
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// Shared, not copied, across dataset snapshots: the mask is constant for a run, so a per-frame
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// dataset refresh / mutable copy must not clone the full-detector (~tens of MB) mask. Held as
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// shared_ptr<const>; the rare edit (user mask) builds a fresh mask (copy-on-write). Never null.
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std::shared_ptr<const PixelMask> pixel_mask = std::make_shared<const PixelMask>();
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std::optional<int64_t> error_value;
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// The master file's detect_ice_rings key, kept as written rather than collapsed to a bool, so a
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// consumer can tell "the file asked for this" from "the file said nothing". Offline processing
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// defaults ice handling by geometry when the file is silent (see rugnux_cli).
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std::optional<bool> file_detect_ice_rings;
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std::string jfjoch_release;
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// Change of basis (3x3 integers, row major) from the setting the per-image reflections and
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// lattices in this file were written in to the setting of experiment's unit cell and space group:
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// hkl_cell = M . hkl_written. The per-image data are written as each image is processed, but the
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// space group - and the conventional setting that comes with it - is only settled after the merge,
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// so the two are not always the same setting. Empty means they are. Read straight from
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// /entry/MX/reindexMatrix; the reader applies it, so everything this class hands out is already in
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// the cell's setting.
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std::optional<std::array<int32_t, 9>> reindex_matrix;
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std::vector<float> az_int_bin_to_q;
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std::vector<float> az_int_bin_to_phi;
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size_t azimuthal_bins = 0;
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size_t q_bins = 0;
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std::vector<float> spot_count;
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std::vector<float> spot_count_indexed;
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std::vector<float> spot_count_low_res;
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std::vector<float> spot_count_ice_rings;
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std::vector<float> spot_count_ice_control;
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std::vector<float> indexing_result;
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std::vector<float> indexing_lattice_count;
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std::vector<float> bkg_estimate;
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// NaN entries are frames with no value (CANNOT SAY), not zeros.
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std::vector<float> spindle_blind_fraction;
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std::vector<float> ice_ring_score;
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std::vector<float> resolution_estimate;
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std::vector<float> efficiency;
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std::vector<float> profile_radius;
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std::vector<float> mosaicity_deg;
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std::vector<float> b_factor;
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std::vector<float> integrated_reflections;
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std::vector<float> image_scale_factor;
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std::vector<float> image_scale_cc;
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std::vector<int64_t> max_value;
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// Per-image sweep-quality code from /entry/MX/sweepQuality: 0 = the image is in no flagged range,
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// otherwise a 1-based index into sweep_quality_reasons (the vocabulary stored beside it, so the
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// codes read back without this source). Both empty when the file carries no sweep quality, which
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// means the run never looked - not that every image was clean.
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std::vector<uint8_t> sweep_quality;
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std::vector<std::string> sweep_quality_reasons;
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// Maps this dataset's image index -> the original/collected image number it came from.
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// Empty means identity (image i == original image i). Lets a dataset be a subset (or strided
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// selection) of the truly collected images: reprocessing snapshots over a sub-range, and (in
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// future) a main dataset that was filtered on-the-fly during collection.
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std::vector<int> source_image_number;
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std::vector<std::string> roi;
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std::vector<std::vector<int64_t>> roi_sum;
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std::vector<std::vector<int64_t>> roi_sum_sq;
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std::vector<std::vector<int64_t>> roi_max;
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std::vector<std::vector<int64_t>> roi_npixel;
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std::vector<std::vector<float>> roi_x;
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std::vector<std::vector<float>> roi_y;
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// ROI definitions stored in the master file. The logical definitions populate
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// experiment.ROI() (they re-derive with the current geometry); roi_map is the
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// per-pixel bitmask as written (constant footprint), with roi_bit_index mapping
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// each ROI name to its bit.
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std::vector<uint16_t> roi_map;
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std::map<std::string, uint16_t> roi_bit_index;
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std::vector<std::string> calibration_data;
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JFJochReaderDataset() = default;
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JFJochReaderDataset(const JFJochReaderDataset &other) = default;
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};
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