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* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
40 lines
2.0 KiB
C++
40 lines
2.0 KiB
C++
// SPDX-FileCopyrightText: 2026 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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// Included only under JFJOCH_USE_CUDA.
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#include <cstdint>
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#include <vector>
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#include <cuda_runtime.h>
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// What the mask is drawn about: the detector, the beam centre, and the geometry the rings and the
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// polarization factor are read off (ShadowFinder keeps it as a DiffractionGeometry; the device takes
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// it as numbers).
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struct ShadowMaskSetup {
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int width = 0, height = 0;
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float beam_x = 0.0f, beam_y = 0.0f;
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float det_matrix[9] = {}; // row major
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float pixel_size_mm = 0.0f;
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float distance_mm = 0.0f;
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bool has_polarization = false;
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float polarization = 0.0f;
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};
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// ShadowFinder::GetMask on the device, from the projection ShadowAccumulatorGPU holds there. Step for
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// step the host's algorithm - the same pooling, ring medians, components, morphology and arm search -
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// and the same answer wherever the arithmetic is exact: every integer, comparison, sort and component
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// is. What is not is the floating point the two compilers evaluate differently - the polarization
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// factor's trigonometry, the Poisson test's logarithm and the azimuth of the arm search - so a pixel
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// within a rounding of one of those thresholds can come out the other way.
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std::vector<uint32_t> ShadowMaskOnDevice(const ShadowMaskSetup &setup, const std::vector<uint32_t> &pixel_mask,
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const int64_t *max_value, const int64_t *sum_value,
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const uint32_t *valid_count, uint32_t frames, cudaStream_t stream);
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// The mean projection the host's GetMeanProjection makes, computed where the sums are: the same
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// division, so the same bits, and a quarter of the bytes to bring back.
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std::vector<float> MeanProjectionOnDevice(const std::vector<uint32_t> &pixel_mask, const int64_t *sum_value,
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const uint32_t *valid_count, size_t npixels, cudaStream_t stream);
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