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Jungfraujoch/image_analysis/image_preprocessing/ImagePreprocessorBufferGPU.cu
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leonarski_fandClaude Opus 5.5 0a515bb086 rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG
The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, as one change on main. The individual commits stay on the rc178 branch:

- still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes
- AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets
- DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
- tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout
- Dense per-pixel maps through the panel table (panel layout stage 1)
- Panel id on spots and the panel table in the start message
- Viewer and preview show a panel detector as it lies on the detector plane
- Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
- Panel layout stage 2: prediction and Bragg integration through the panel table
- XTC reader: frames handed up as stored, streams indexed in parallel
- XFEL reader: integer frames stay integer, one gain, placement by panel
- EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery"
- still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed
- float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count
- CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them
- Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table
- Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane
- still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good
- still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file
- still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition
- stills fixed cost: geometry refinement and pre-scan do the same work in less wall time
- stills geometry sample and trial spot finding run as many workers as the image pass
- Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame
- StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's
- MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in)
- Stills given a cell: the written cell is the mean over the frames that are merged
- Stills: the radial curvature correction decided per run on the same empty apertures
- StillsPartialityRefine: measure the run width only on shells with signal
- Stills pre-scan: report the paired z of the radial-correction comparison
- module placement: the five concurrent fits each keep every thread
- still battery: score R-free against the deposited data through the same dimple protocol
- still battery: the R-free target is the lower of the deposition's dimple and published values
- Stills: background clip follows the radial curve; signal disk from the lattice spacing
- Stills keep an overloaded observation as a lower bound instead of dropping it
- Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip
- battery: R-free against the deposition without refinement only, one protocol for rotation and stills
- still battery: EuXFEL sets run on a 2,000-image subset for now
- stills geometry refinement: fit the detector distance and the cell together
- stills geometry refinement: a distance given with --detector-distance is held in the joint fit
- Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count
- Metal integration test: the CPU comparison runs on a rotation experiment
- Stills: kept overloads go back to the drop where they are not concentrated at low resolution
- stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated
- battery results: XFEL still battery 20261022-1358 on rc178 0cf62452c - 12 sets, cold, R_free unrefined
- battery results: still summary gains the resolution of our merge and of the deposition
- Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value
- Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed
- XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock
- stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes
- rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid
- stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree
- CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get
- broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4)
- frontend: Mol* viewer of the placed model and its density on the Rugnux live page
- writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does
- rugnux live maps: one unit cell centred on the model; the viewer opens on all of it
- Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer
- Mol* viewer: open with the maps drawn within 10 A of the centre of view
- Mol* viewer: aaredb's structure-viewer setup, on a black stage
- rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons
- Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2)
- ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI)
- stills tilt decision: the modules stay where the run placed them
- still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it
- battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC
- Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons
- BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it
- ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization
- BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain
- ShadowFinder: measure the modulation robustly under a wide one-sided shadow
- ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation
- ShadowFinder: back to the predicted polarization factor, in the plane the background shows
- MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again
- battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables
- XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel
- stills geometry trial: the hypotheses a search asks are indexed side by side
- stills tilt decision: the fits start beside the pre-scan and the geometry trial
- XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache
- XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step
- GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block
- GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart
- docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts
- battery: doc_check.py cross-checks the manifests against the dataset pages
- stills module placement: the placement fit gets half the threads, each held-out fit an eighth
- still battery: the EuXFEL sets run on all their frames, as the published still runs did
- battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table
- macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
2026-10-23 17:56:42 +02:00

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// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "ImagePreprocessorBufferGPU.h"
#include <algorithm>
#include <climits>
static inline void cuda_err(cudaError_t val) {
if (val != cudaSuccess)
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}
__global__ void gather_kernel(const int32_t *__restrict__ image,
const uint32_t *__restrict__ npixel,
int32_t *__restrict__ values,
int count) {
for (int i = blockIdx.x * blockDim.x + threadIdx.x; i < count; i += blockDim.x * gridDim.x)
values[i] = image[npixel[i]];
}
// centre holds six values per tile: its centre x, y and the box x0, y0, x1, y1 it is clipped to.
__global__ void gather_tiles_kernel(const int32_t *__restrict__ image, int width,
const int32_t *__restrict__ centre, int half,
int32_t *__restrict__ tiles, size_t count) {
const int side = 2 * half + 1;
const size_t area = static_cast<size_t>(side) * side;
for (size_t i = blockIdx.x * blockDim.x + threadIdx.x; i < count; i += static_cast<size_t>(blockDim.x) * gridDim.x) {
const size_t tile = i / area;
const int p = static_cast<int>(i - tile * area);
const int32_t *c = centre + 6 * tile;
const int px = c[0] - half + p % side;
const int py = c[1] - half + p / side;
tiles[i] = (px < c[2] || py < c[3] || px >= c[4] || py >= c[5])
? INT32_MIN : image[static_cast<size_t>(py) * width + px];
}
}
ImagePreprocessorBufferGPU::ImagePreprocessorBufferGPU(size_t npixel, bool host_mirror)
: ImagePreprocessorBuffer(npixel, host_mirror),
gpu_image(npixel),
// A no-op when the mirror was not allocated: CudaRegisteredVector skips an empty vector.
buffer_reg(buffer),
max_gather(StrongPixelLimit(npixel)),
gpu_gather_index(max_gather),
gpu_gather_value(max_gather) {
}
int32_t *ImagePreprocessorBufferGPU::getGPUBuffer() {
return gpu_image;
}
const int32_t *ImagePreprocessorBufferGPU::getGPUBuffer() const {
return gpu_image;
}
void ImagePreprocessorBufferGPU::Gather(const std::vector<uint32_t> &npixel, std::vector<int32_t> &values) const {
values.resize(npixel.size());
if (npixel.empty())
return;
const int count = static_cast<int>(npixel.size());
cudaMemcpyAsync(gpu_gather_index.get(), npixel.data(), count * sizeof(uint32_t),
cudaMemcpyHostToDevice, gather_stream);
gather_kernel<<<(count + 255) / 256, 256, 0, gather_stream>>>(
gpu_image.get(), gpu_gather_index.get(), gpu_gather_value.get(), count);
cuda_err(cudaGetLastError());
cudaMemcpyAsync(values.data(), gpu_gather_value.get(), count * sizeof(int32_t),
cudaMemcpyDeviceToHost, gather_stream);
cudaStreamSynchronize(gather_stream);
}
const int32_t *ImagePreprocessorBufferGPU::GatherTiles(const std::vector<int32_t> &x, const std::vector<int32_t> &y,
int width, int half) {
const size_t side = 2 * half + 1;
const size_t count = x.size() * side * side;
if (count == 0)
return nullptr;
if (count > tile_capacity) {
tile_capacity = std::max(count, 2 * tile_capacity);
gpu_tiles = CudaDevicePtr<int32_t>(tile_capacity);
host_tiles.resize(tile_capacity);
}
if (6 * x.size() > tile_centre.size()) {
tile_centre.resize(std::max(6 * x.size(), 2 * tile_centre.size()));
gpu_tile_centre = CudaDevicePtr<int32_t>(tile_centre.size());
}
for (size_t i = 0; i < x.size(); i++) {
const PanelBox b = TileBox(x[i], y[i], width);
int32_t *c = tile_centre.data() + 6 * i;
c[0] = x[i];
c[1] = y[i];
c[2] = b.x0;
c[3] = b.y0;
c[4] = b.x1;
c[5] = b.y1;
}
cuda_err(cudaMemcpyAsync(gpu_tile_centre.get(), tile_centre.data(), 6 * x.size() * sizeof(int32_t),
cudaMemcpyHostToDevice, gather_stream));
const int blocks = static_cast<int>(std::min<size_t>((count + 255) / 256, 4096));
gather_tiles_kernel<<<blocks, 256, 0, gather_stream>>>(gpu_image.get(), width,
gpu_tile_centre.get(), half, gpu_tiles.get(), count);
cuda_err(cudaGetLastError());
cuda_err(cudaMemcpyAsync(host_tiles.data(), gpu_tiles.get(), count * sizeof(int32_t),
cudaMemcpyDeviceToHost, gather_stream));
cuda_err(cudaStreamSynchronize(gather_stream));
return host_tiles.data();
}
const int32_t *ImagePreprocessorBufferGPU::HostImage() {
buffer.resize(npixels);
cuda_err(cudaMemcpyAsync(buffer.data(), gpu_image.get(), npixels * sizeof(int32_t),
cudaMemcpyDeviceToHost, gather_stream));
cuda_err(cudaStreamSynchronize(gather_stream));
return buffer.data();
}