Jungfraujoch/common/Definitions.h

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#pragma once

#include "../fpga/pcie_driver/jfjoch_fpga.h"

#include <cstdint>
#include <cstddef>
#include <chrono>
#include <array>
#include <cmath>

constexpr float WVL_1A_IN_KEV = 12.39854f;

constexpr size_t CONVERTED_MODULE_LINES = 514;
constexpr size_t CONVERTED_MODULE_COLS = 1030;
constexpr size_t CONVERTED_MODULE_SIZE = CONVERTED_MODULE_LINES * CONVERTED_MODULE_COLS;
constexpr size_t JUNGFRAU_PACKET_SIZE_BYTES = 8192;

constexpr int MAX_IMAGE_NUMBER = 2*1024*1024;

// Defaults for images_per_file when the acquisition does not ask for a particular number; see
// DiffractionExperiment::GetImagesPerFile.
constexpr int64_t DEFAULT_IMAGES_PER_FILE = 1000;
// Above this, a rotation sweep is split rather than written to one file.
constexpr int64_t ROTATION_SINGLE_FILE_IMAGE_LIMIT = 20000;

constexpr std::chrono::nanoseconds MIN_COUNT_TIME = std::chrono::microseconds(3);
constexpr std::chrono::nanoseconds MIN_STORAGE_CELL_DELAY = std::chrono::nanoseconds(2100);
constexpr std::chrono::nanoseconds MIN_FRAME_TIME_JUNGFRAU_HALF_SPEED = std::chrono::microseconds(1000);
constexpr std::chrono::nanoseconds MIN_FRAME_TIME_JUNGFRAU_FULL_SPEED = std::chrono::microseconds(470);
constexpr std::chrono::nanoseconds MIN_FRAME_TIME_EIGER = std::chrono::microseconds(250);
constexpr std::chrono::nanoseconds MAX_COUNT_TIME_JUNGFRAU = std::chrono::microseconds(2000);
constexpr std::chrono::nanoseconds FRAME_TIME_PEDE_G1G2 = std::chrono::microseconds(10*1000);

constexpr std::chrono::nanoseconds PSI_JUNGFRAU_READOUT_TIME = std::chrono::microseconds(20);
constexpr std::chrono::nanoseconds PSI_EIGER_READOUT_TIME = std::chrono::microseconds(20);
constexpr std::chrono::nanoseconds DARK_MASK_FRAME_TIME = std::chrono::milliseconds(10);

constexpr float MIN_ENERGY_KEV = 0.001;
constexpr float MAX_ENERGY_KEV = 500.0;

constexpr float DEFAULT_G0_FACTOR = 41.0f;
constexpr float DEFAULT_G1_FACTOR = -1.439f;
constexpr float DEFAULT_G2_FACTOR = -0.1145f;
constexpr float DEFAULT_HG0_FACTOR = 100.0f;

constexpr int MAX_SPOT_COUNT = 64 * 1024;

// Three spots fit any lattice at all; one short of ViableCellMinSpots (default 9) is where a fitted
// lattice stops being distinguishable from a random one, so a spot list shorter than this is never
// worth handing to indexing - and the frame gate needs the same count to validate a frame
// (AnalyzeIndexing), so a shorter list could never index anything anyway.
constexpr int MIN_SPOT_COUNT = 10;

constexpr uint32_t MASK_PEDESTAL_G0_RMS_LIMIT = (1U<<4);

constexpr size_t PEDESTAL_MIN_IMAGE_COUNT = 128;
constexpr uint16_t PEDESTAL_WRONG = (UINT16_MAX);
constexpr size_t PEDESTAL_G0_WRONG_GAIN_ALLOWED_COUNT = 2;

constexpr size_t MESSAGE_SIZE_FOR_START_END = (256*1024*1024); // pessimistic highest value
constexpr float LAB6_CELL_A = 4.156468f;

// Hexagonal-ice ring positions. The first eleven are the measured ones from:
// Moreau, Atakisi, Thorne, Acta Cryst D77, 2021, 540,554
// https://journals.iucr.org/d/issues/2021/04/00/tz5104/index.html
// That paper's Table 1 stops at 1.522 A because it says so in its own words - "pure hexagonal ice has
// 11 diffraction rings between 4 and 1.5 A resolution" - and its subject was detecting ice in the PDB,
// not masking it. Ice does not stop there, and on a detector that reaches past 1.5 A the rings it does
// not list are the ones left in the data: one strongly diffracting set had 44% of every frame's spots
// in ice bands, and beyond 1.5 A its spots were ice and nothing else.
//
// The rest are calculated, because past that paper there is nothing measured to copy. Ice Ih is
// P6_3/mmc with O on 4f, so enumerating hkl is not enough - most of what it emits is extinguished by
// the oxygen sublattice rather than by the space group, which is why (004) at 1.830 A and (104) at
// 1.657 A are absent from the measured list although they lie inside its range and its reflection
// conditions allow them. Structure factors were computed instead (oxygen only - the hydrogens are
// half-occupancy disordered and scatter X-rays weakly) and the lines kept are those reaching 3% of the
// strongest. That reproduces the measured eleven exactly, and every line it drops in their range
// computes to zero, which is what makes the same rule trustworthy below 1.522 A.
// Following Roettger, Endriss, Ihringer, Doyle & Kuhs (1994) Acta Cryst. B50, 644-648 for the cell.
//
// It stops at 1.170 A: below that the calculated real lines fall to 2-3% while the extinct ones rise
// to about 1%, and an oxygen-only calculation cannot separate them honestly any further.
constexpr std::array<float, 19> ICE_RING_RES_A = {3.895, 3.661, 3.438, 2.667, 2.249, 2.068, 1.947,
                                                  1.916, 1.882, 1.719, 1.522,
                                                  1.472, 1.443, 1.371, 1.366, 1.298, 1.261, 1.224,
                                                  1.170};

// Cubic-ice (Ic) ring positions, d = a / sqrt(h^2+k^2+l^2) with a = 6.358 A and the diamond-lattice
// reflection conditions (hkl all odd, or all even with h+k+l = 4n). Flash-cooled loops show cubic or
// stacking-disordered ice at least as often as hexagonal, and the two phases share only three lines,
// so a detector that only looks for ICE_RING_RES_A above misses it. Used by the ice detection score
// as a second, independent hypothesis - not by the spot ice-ring flag, which stays hexagonal because
// masking on a phase that is usually absent would throw away good reflections.
constexpr std::array<float, 9> ICE_RING_CUBIC_RES_A = {3.670, 2.248, 1.917, 1.835, 1.590,
                                                       1.459, 1.298, 1.224, 1.124};

// True when resolution d (Angstrom) sits within half_width of a hexagonal-ice powder ring, in the
// q = 2*pi/d units the spot-finder uses (ice_ring_width_Q_recipA). Used to drop ice-contaminated
// reflections from scaling/merging when ice-ring handling is enabled.
inline bool IsOnIceRing(float d_A, float half_width_q_recipA) {
    if (!(d_A > 0.0f))
        return false;
    constexpr float two_pi = 6.283185307f;
    const float q = two_pi / d_A;
    for (const float ice_d : ICE_RING_RES_A)
        if (std::fabs(q - two_pi / ice_d) < half_width_q_recipA)
            return true;
    return false;
}