Jungfraujoch/reader/JFJochReaderDataset.h

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include <string>
#include <array>
#include <optional>
#include <vector>
#include <map>
#include <memory>

#include "../common/DiffractionGeometry.h"
#include "../common/DiffractionExperiment.h"
#include "../common/PixelMask.h"
#include "../common/AzimuthalIntegrationMapping.h"

struct JFJochReaderDataset {
    std::string arm_date;

    DiffractionExperiment experiment;
    // Shared, not copied, across dataset snapshots: the mask is constant for a run, so a per-frame
    // dataset refresh / mutable copy must not clone the full-detector (~tens of MB) mask. Held as
    // shared_ptr<const>; the rare edit (user mask) builds a fresh mask (copy-on-write). Never null.
    std::shared_ptr<const PixelMask> pixel_mask = std::make_shared<const PixelMask>();

    std::optional<int64_t> error_value;

    // The master file's detect_ice_rings key, kept as written rather than collapsed to a bool, so a
    // consumer can tell "the file asked for this" from "the file said nothing". Offline processing
    // defaults ice handling by geometry when the file is silent (see rugnux_cli).
    std::optional<bool> file_detect_ice_rings;

    std::string jfjoch_release;

    // Change of basis (3x3 integers, row major) from the setting the per-image reflections and
    // lattices in this file were written in to the setting of experiment's unit cell and space group:
    // hkl_cell = M . hkl_written. The per-image data are written as each image is processed, but the
    // space group - and the conventional setting that comes with it - is only settled after the merge,
    // so the two are not always the same setting. Empty means they are. Read straight from
    // /entry/MX/reindexMatrix; the reader applies it, so everything this class hands out is already in
    // the cell's setting.
    std::optional<std::array<int32_t, 9>> reindex_matrix;

    std::vector<float> az_int_bin_to_q;
    std::vector<float> az_int_bin_to_phi;
    size_t azimuthal_bins = 0;
    size_t q_bins = 0;

    std::vector<float> spot_count;
    std::vector<float> spot_count_indexed;
    std::vector<float> spot_count_low_res;
    std::vector<float> spot_count_ice_rings;
    std::vector<float> spot_count_ice_control;

    std::vector<float> indexing_result;
    std::vector<float> indexing_lattice_count;
    std::vector<float> bkg_estimate;
    std::vector<float> ice_ring_score;
    // The two per-image detection scores, in [0,1] and saturating: is there protein diffraction on
    // this image, and is there crystalline ice. From /entry/MX/proteinScore and /entry/MX/iceScore;
    // empty when the file predates them. score_beam_center_x/y is the beam centre they were computed
    // with, which is NOT necessarily the refined one the geometry above carries.
    std::vector<float> protein_score;
    std::vector<float> ice_score;
    std::optional<float> score_beam_center_x;
    std::optional<float> score_beam_center_y;
    std::vector<float> resolution_estimate;
    std::vector<float> efficiency;
    std::vector<float> profile_radius;
    std::vector<float> mosaicity_deg;
    std::vector<float> b_factor;
    std::vector<float> integrated_reflections;
    std::vector<float> image_scale_factor;
    std::vector<float> image_scale_cc;
    std::vector<int64_t> max_value;

    // Per-image sweep-quality code from /entry/MX/sweepQuality: 0 = the image is in no flagged range,
    // otherwise a 1-based index into sweep_quality_reasons (the vocabulary stored beside it, so the
    // codes read back without this source). Both empty when the file carries no sweep quality, which
    // means the run never looked - not that every image was clean.
    std::vector<uint8_t> sweep_quality;
    std::vector<std::string> sweep_quality_reasons;

    // Maps this dataset's image index -> the original/collected image number it came from.
    // Empty means identity (image i == original image i). Lets a dataset be a subset (or strided
    // selection) of the truly collected images: reprocessing snapshots over a sub-range, and (in
    // future) a main dataset that was filtered on-the-fly during collection.
    std::vector<int> source_image_number;

    std::vector<std::string> roi;
    std::vector<std::vector<int64_t>> roi_sum;
    std::vector<std::vector<int64_t>> roi_sum_sq;
    std::vector<std::vector<int64_t>> roi_max;
    std::vector<std::vector<int64_t>> roi_npixel;
    std::vector<std::vector<float>> roi_x;
    std::vector<std::vector<float>> roi_y;

    // ROI definitions stored in the master file. The logical definitions populate
    // experiment.ROI() (they re-derive with the current geometry); roi_map is the
    // per-pixel bitmask as written (constant footprint), with roi_bit_index mapping
    // each ROI name to its bit.
    std::vector<uint16_t> roi_map;
    std::map<std::string, uint16_t> roi_bit_index;

    std::vector<std::string> calibration_data;

    JFJochReaderDataset() = default;
    JFJochReaderDataset(const JFJochReaderDataset &other) = default;
};