leonarski_fandClaude Opus 5
64169bb04d
The rotation first pass measures how deep each image's intensity-ordered spot list still lies on the lattice and adopts that depth as the spot budget. The measurement can honestly land below ten - seen where a wrong header detector distance left indexing a compensating, uniformly scaled cell that matches only the few brightest, most central spots - but the setter rejects anything under ten, so the run died on its own measurement, reporting a parameter the user never set. The floor predates the estimator by a year and was written to guard user input; by provenance it is the stills fitting bound, one more than a viable cell needs, which a rotation pass that only tests a lattice already in hand does not owe anything to. Exempting the measurement entirely would be worse than the crash: the validation gate still needs that many indexed spots per frame, so a shorter list can never index anything and the pass would abort one confusing error later. So the floor gets a name beside its companion, keeps its job for input, and the measured budget is clamped to it before adoption - with a warning saying what a sub-floor measurement means: the geometry in the file or the lattice is wrong, not that the crystal is weak. The dataset that died now completes like its siblings with the cause named; the same data at the reference-refined distance indexes 99% of images and measures no budget cut at all; and runs whose budgets sit at or above the floor are report-identical, checked at the two lowest in the corpus. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
105 lines
5.5 KiB
C++
105 lines
5.5 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 "../fpga/pcie_driver/jfjoch_fpga.h"
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#include <cstdint>
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#include <cstddef>
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#include <chrono>
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#include <array>
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#include <cmath>
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constexpr float WVL_1A_IN_KEV = 12.39854f;
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constexpr size_t CONVERTED_MODULE_LINES = 514;
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constexpr size_t CONVERTED_MODULE_COLS = 1030;
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constexpr size_t CONVERTED_MODULE_SIZE = CONVERTED_MODULE_LINES * CONVERTED_MODULE_COLS;
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constexpr size_t JUNGFRAU_PACKET_SIZE_BYTES = 8192;
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constexpr int MAX_IMAGE_NUMBER = 2*1024*1024;
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// Defaults for images_per_file when the acquisition does not ask for a particular number; see
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// DiffractionExperiment::GetImagesPerFile.
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constexpr int64_t DEFAULT_IMAGES_PER_FILE = 1000;
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// Above this, a rotation sweep is split rather than written to one file.
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constexpr int64_t ROTATION_SINGLE_FILE_IMAGE_LIMIT = 20000;
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constexpr std::chrono::nanoseconds MIN_COUNT_TIME = std::chrono::microseconds(3);
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constexpr std::chrono::nanoseconds MIN_STORAGE_CELL_DELAY = std::chrono::nanoseconds(2100);
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constexpr std::chrono::nanoseconds MIN_FRAME_TIME_JUNGFRAU_HALF_SPEED = std::chrono::microseconds(1000);
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constexpr std::chrono::nanoseconds MIN_FRAME_TIME_JUNGFRAU_FULL_SPEED = std::chrono::microseconds(470);
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constexpr std::chrono::nanoseconds MIN_FRAME_TIME_EIGER = std::chrono::microseconds(250);
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constexpr std::chrono::nanoseconds MAX_COUNT_TIME_JUNGFRAU = std::chrono::microseconds(2000);
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constexpr std::chrono::nanoseconds FRAME_TIME_PEDE_G1G2 = std::chrono::microseconds(10*1000);
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constexpr std::chrono::nanoseconds PSI_JUNGFRAU_READOUT_TIME = std::chrono::microseconds(20);
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constexpr std::chrono::nanoseconds PSI_EIGER_READOUT_TIME = std::chrono::microseconds(20);
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constexpr std::chrono::nanoseconds DARK_MASK_FRAME_TIME = std::chrono::milliseconds(10);
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constexpr float MIN_ENERGY_KEV = 0.001;
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constexpr float MAX_ENERGY_KEV = 500.0;
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constexpr float DEFAULT_G0_FACTOR = 41.0f;
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constexpr float DEFAULT_G1_FACTOR = -1.439f;
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constexpr float DEFAULT_G2_FACTOR = -0.1145f;
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constexpr float DEFAULT_HG0_FACTOR = 100.0f;
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constexpr int MAX_SPOT_COUNT = 64 * 1024;
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// Three spots fit any lattice at all; one short of ViableCellMinSpots (default 9) is where a fitted
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// lattice stops being distinguishable from a random one, so a spot list shorter than this is never
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// worth handing to indexing - and the frame gate needs the same count to validate a frame
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// (AnalyzeIndexing), so a shorter list could never index anything anyway.
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constexpr int MIN_SPOT_COUNT = 10;
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constexpr uint32_t MASK_PEDESTAL_G0_RMS_LIMIT = (1U<<4);
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constexpr size_t PEDESTAL_MIN_IMAGE_COUNT = 128;
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constexpr uint16_t PEDESTAL_WRONG = (UINT16_MAX);
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constexpr size_t PEDESTAL_G0_WRONG_GAIN_ALLOWED_COUNT = 2;
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constexpr size_t MESSAGE_SIZE_FOR_START_END = (256*1024*1024); // pessimistic highest value
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constexpr float LAB6_CELL_A = 4.156468f;
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// Hexagonal-ice ring positions. The first eleven are the measured ones from:
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// Moreau, Atakisi, Thorne, Acta Cryst D77, 2021, 540,554
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// https://journals.iucr.org/d/issues/2021/04/00/tz5104/index.html
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// That paper's Table 1 stops at 1.522 A because it says so in its own words - "pure hexagonal ice has
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// 11 diffraction rings between 4 and 1.5 A resolution" - and its subject was detecting ice in the PDB,
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// not masking it. Ice does not stop there, and on a detector that reaches past 1.5 A the rings it does
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// not list are the ones left in the data: one strongly diffracting set had 44% of every frame's spots
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// in ice bands, and beyond 1.5 A its spots were ice and nothing else.
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//
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// The rest are calculated, because past that paper there is nothing measured to copy. Ice Ih is
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// P6_3/mmc with O on 4f, so enumerating hkl is not enough - most of what it emits is extinguished by
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// the oxygen sublattice rather than by the space group, which is why (004) at 1.830 A and (104) at
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// 1.657 A are absent from the measured list although they lie inside its range and its reflection
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// conditions allow them. Structure factors were computed instead (oxygen only - the hydrogens are
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// half-occupancy disordered and scatter X-rays weakly) and the lines kept are those reaching 3% of the
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// strongest. That reproduces the measured eleven exactly, and every line it drops in their range
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// computes to zero, which is what makes the same rule trustworthy below 1.522 A.
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// Following Roettger, Endriss, Ihringer, Doyle & Kuhs (1994) Acta Cryst. B50, 644-648 for the cell.
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//
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// It stops at 1.170 A: below that the calculated real lines fall to 2-3% while the extinct ones rise
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// to about 1%, and an oxygen-only calculation cannot separate them honestly any further.
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constexpr std::array<float, 19> ICE_RING_RES_A = {3.895, 3.661, 3.438, 2.667, 2.249, 2.068, 1.947,
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1.916, 1.882, 1.719, 1.522,
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1.472, 1.443, 1.371, 1.366, 1.298, 1.261, 1.224,
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1.170};
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// True when resolution d (Angstrom) sits within half_width of a hexagonal-ice powder ring, in the
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// q = 2*pi/d units the spot-finder uses (ice_ring_width_Q_recipA). Used to drop ice-contaminated
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// reflections from scaling/merging when ice-ring handling is enabled.
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inline bool IsOnIceRing(float d_A, float half_width_q_recipA) {
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if (!(d_A > 0.0f))
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return false;
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constexpr float two_pi = 6.283185307f;
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const float q = two_pi / d_A;
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for (const float ice_d : ICE_RING_RES_A)
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if (std::fabs(q - two_pi / ice_d) < half_width_q_recipA)
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return true;
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return false;
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}
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