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Jungfraujoch/common/Definitions.h
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v1.0.0.rc-162 (#72)
**Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one.

* HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected.
* HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it.
* HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset.
* HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts.
* HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout.
* A grid scan and a goniometer axis can both be set; they are no longer alternatives.
* `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000.
* The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned.
* The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer.
* rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it.
* rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`.
* rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way.
* rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound.
* rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached.
* rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use.
* rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own.
* rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement.
* rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged.
* rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged.
* Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged.
* A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses.
* rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given.
* CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer.
* The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2.
* Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact.

**Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`):
* `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file.
* `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them.

---------

Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch>
Reviewed-on: #72
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-25 08:21:39 +02:00

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// 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;
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;
// Ice ring resolution taken from:
// Moreau, Atakisi, Thorne, Acta Cryst D77, 2021, 540,554
// https://journals.iucr.org/d/issues/2021/04/00/tz5104/index.html
constexpr std::array<float, 11> 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};
// 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;
}