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Jungfraujoch/image_analysis/image_preprocessing/BSLZ4DecodeWarp.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

129 lines
6.8 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <cstdint>
// The LZ4 block parser, as a device function, so the standalone decode kernel and the fused
// decode+un-transpose+preprocess kernel run exactly the same code over the same bytes. The two
// differ only in where the output lands - device memory for the first, a shared-memory staging
// buffer for the second - and a generic pointer covers both, so there is one parser and no way for
// the two paths to disagree on what a chunk decodes to.
//
// CUDA only: include it from a .cu, never from a header a .cpp sees.
// One WARP per LZ4 block. Every lane runs the same sequence parser over the same bytes - a
// broadcast read, so no divergence - and the literal and match copies are split across the 32
// lanes so the stores coalesce. One thread per block instead has each thread streaming its own
// 8 kB region, which coalesces not at all and measured 13x slower.
//
// Because the lanes cooperate on the copies, a match can source bytes that OTHER lanes wrote in
// an earlier sequence. Since Volta that needs an explicit __syncwarp() - implicit reconvergence
// is not part of the programming model - so there is one after every copy loop. The full mask is
// correct: the early return and every break test warp-uniform values, so lanes never diverge
// permanently.
//
// Bounds: every read is clamped against iend and every write against oend, so a malformed or
// corrupt payload cannot walk off either buffer. It can still stop early, which leaves the block
// short; that is what the false return reports.
__device__ __forceinline__ bool lz4_decode_block_warp(const uint8_t *ip, const uint8_t *const iend,
uint8_t *const obase, uint8_t *const oend,
int lane) {
uint8_t *op = obase;
bool malformed = false;
while (ip < iend) {
const uint32_t token = *ip++;
uint32_t litlen = token >> 4;
if (litlen == 15) {
// read_variable_length(&ip, iend - RUN_MASK, initial_check=1) in the reference: the
// chain may not start within, nor run into, the last RUN_MASK (15) input bytes. A
// valid stream never does - the literals it counts have to follow it - so a chain
// that reaches there is corruption, and this is the only place it shows up.
if ((size_t)(iend - ip) <= 15) { malformed = true; break; }
uint32_t s;
do {
s = *ip++;
litlen += s;
if ((size_t)(iend - ip) < 15) { malformed = true; break; }
} while (s == 255);
if (malformed) break;
}
if (litlen) {
// Clamped by the INPUT as well as the output: a corrupt litlen must not read past the
// end of this block's payload or write past the end of the block. Clamping keeps the
// kernel in bounds; needing to clamp at all means the stream is not decodable, which
// is what the reference reports as an error, so record it.
if (litlen > (uint32_t)(oend - op) || litlen > (uint32_t)(iend - ip))
malformed = true;
const uint32_t n = min(min(litlen, (uint32_t)(oend - op)), (uint32_t)(iend - ip));
for (uint32_t i = lane; i < n; i += 32) op[i] = ip[i];
__syncwarp();
op += n; ip += litlen;
}
// LZ4's parsing restrictions: an encoder may not leave a match within MFLIMIT (12) bytes
// of the end of the block, nor fewer than 2+1+LASTLITERALS (8) input bytes after a
// literal run that is not the last one. So once either limit is reached this can ONLY be
// the final sequence, and the final sequence must consume the payload exactly. The
// reference applies this whether or not the run was empty, which is why the test sits
// outside the copy - a zero-length literal run near the end is just as illegal.
if ((size_t)(oend - op) < 12 || (size_t)(iend - ip) < 8) {
malformed = (ip != iend) || (op != oend);
break; // necessarily EOF
}
if (iend - ip < 2) break; // last sequence carries literals only
const uint32_t offset = (uint32_t)ip[0] | ((uint32_t)ip[1] << 8);
ip += 2;
uint32_t matchlen = token & 0x0F;
if (matchlen == 15) {
// read_variable_length(&ip, iend - LASTLITERALS + 1, initial_check=0): bounded by the
// last 4 input bytes rather than 15, and with no check before the first read.
uint32_t s;
do {
s = *ip++;
matchlen += s;
if ((size_t)(iend - ip) < 4) { malformed = true; break; }
} while (s == 255);
if (malformed) break;
}
matchlen += 4; // minmatch
if (offset == 0 || offset > (uint32_t)(op - obase)) { malformed = true; break; }
const uint8_t *mp = op - offset;
// A match may reach the end of the block but never past it - the reference treats an
// overrun as an error rather than truncating, and so must this.
if (matchlen > (uint32_t)(oend - op))
malformed = true;
const uint32_t n = min(matchlen, (uint32_t)(oend - op));
if (offset >= matchlen) {
for (uint32_t i = lane; i < n; i += 32) op[i] = mp[i];
} else {
// An overlapping match is a pattern of period `offset`. mp[0..offset-1] all lie
// before op and are already final, so each output byte can be sourced from them
// independently - which keeps this parallel rather than a serial byte loop. Long
// zero runs in sparse detector data arrive here with offset == 1, and a runtime
// modulo is an emulated division, so the two cheap cases are peeled off first.
if (offset == 1) {
const uint8_t v = mp[0];
for (uint32_t i = lane; i < n; i += 32) op[i] = v;
} else if ((offset & (offset - 1)) == 0) {
const uint32_t m = offset - 1;
for (uint32_t i = lane; i < n; i += 32) op[i] = mp[i & m];
} else {
for (uint32_t i = lane; i < n; i += 32) op[i] = mp[i % offset];
}
}
__syncwarp();
op += n;
}
// A block must decode to exactly its declared length AND consume exactly its payload. Both
// are conditions LZ4_decompress_safe reports to the host path, and both are needed: a corrupt
// stream can land on the right output length while leaving input over, or run its input out
// early. Either way the bytes are not the ones that were compressed.
return !malformed && op == oend && ip == iend;
}