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Jungfraujoch/image_analysis/roi/ROIIntegrationGPU.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 <climits>
#include "ROIIntegrationGPU.h"
#include "../../common/DiffractionExperiment.h"
inline void cuda_err(cudaError_t val) {
if (val != cudaSuccess)
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}
// One pixel carries a 16-bit mask, so it can feed any subset of the ROIs.
// Each block reduces into shared memory first to keep global atomics low.
// The weighted sums go per ROI and panel (roi * slots + panel; slots = 1 and panel 0 without a panel
// table); panel_box holds x0, y0, width, height of each panel, and a pixel on none is left out.
__global__
void gpu_roi(
const uint16_t *__restrict__ roi_map,
const int32_t *__restrict__ input_buffer,
size_t num_pixels,
size_t width,
int roi_count,
const int *__restrict__ panel_box,
int npanels,
int slots,
unsigned long long *__restrict__ roi_sum,
unsigned long long *__restrict__ roi_sum2,
unsigned long long *__restrict__ roi_pixels,
unsigned long long *__restrict__ roi_panel_v,
unsigned long long *__restrict__ roi_panel_x,
unsigned long long *__restrict__ roi_panel_y,
int *__restrict__ roi_max) {
extern __shared__ unsigned long long shared[];
unsigned long long *s_sum = shared;
unsigned long long *s_sum2 = &s_sum[roi_count];
unsigned long long *s_pixels = &s_sum2[roi_count];
unsigned long long *s_pv = &s_pixels[roi_count];
unsigned long long *s_xw = &s_pv[roi_count * slots];
unsigned long long *s_yw = &s_xw[roi_count * slots];
int *s_max = (int *) &s_yw[roi_count * slots];
for (int r = threadIdx.x; r < roi_count; r += blockDim.x) {
s_sum[r] = 0;
s_sum2[r] = 0;
s_pixels[r] = 0;
s_max[r] = INT_MIN;
}
for (int k = threadIdx.x; k < roi_count * slots; k += blockDim.x) {
s_pv[k] = 0;
s_xw[k] = 0;
s_yw[k] = 0;
}
__syncthreads();
for (size_t idx = blockIdx.x * blockDim.x + threadIdx.x;
idx < num_pixels;
idx += blockDim.x * gridDim.x) {
const uint16_t mask = roi_map[idx];
if (mask == 0)
continue;
const int32_t v = input_buffer[idx];
if (v == INT32_MIN) // masked/bad pixel
continue;
const bool saturated = (v == INT32_MAX);
const long long val = v;
const long long x = idx % width;
const long long y = idx / width;
int panel = 0;
if (npanels > 0) {
panel = -1;
for (int p = 0; p < npanels && panel < 0; p++)
if (x >= panel_box[4 * p] && x < panel_box[4 * p] + panel_box[4 * p + 2]
&& y >= panel_box[4 * p + 1] && y < panel_box[4 * p + 1] + panel_box[4 * p + 3])
panel = p;
if (panel < 0)
continue;
}
const unsigned long long val_u = (unsigned long long) val;
const unsigned long long val2_u = (unsigned long long) (val * val);
const unsigned long long vx_u = (unsigned long long) (val * x);
const unsigned long long vy_u = (unsigned long long) (val * y);
for (int r = 0; r < roi_count; r++) {
if (!(mask & (1u << r)))
continue;
if (!saturated) {
atomicAdd(&s_sum[r], val_u);
atomicAdd(&s_sum2[r], val2_u);
atomicAdd(&s_pixels[r], 1ULL);
atomicAdd(&s_pv[r * slots + panel], val_u);
atomicAdd(&s_xw[r * slots + panel], vx_u);
atomicAdd(&s_yw[r * slots + panel], vy_u);
}
atomicMax(&s_max[r], v);
}
}
__syncthreads();
for (int r = threadIdx.x; r < roi_count; r += blockDim.x) {
atomicAdd(&roi_sum[r], s_sum[r]);
atomicAdd(&roi_sum2[r], s_sum2[r]);
atomicAdd(&roi_pixels[r], s_pixels[r]);
atomicMax(&roi_max[r], s_max[r]);
}
for (int k = threadIdx.x; k < roi_count * slots; k += blockDim.x) {
atomicAdd(&roi_panel_v[k], s_pv[k]);
atomicAdd(&roi_panel_x[k], s_xw[k]);
atomicAdd(&roi_panel_y[k], s_yw[k]);
}
}
ROIIntegrationGPU::ROIIntegrationGPU(const DiffractionExperiment &experiment, std::shared_ptr<CudaStream> stream)
: ROIIntegration(experiment),
stream(stream),
gpu_roi_map(npixel),
gpu_sum(roi_count),
gpu_sum2(roi_count),
gpu_pixels(roi_count),
gpu_panel_v(roi_count * panel_slots),
gpu_panel_x(roi_count * panel_slots),
gpu_panel_y(roi_count * panel_slots),
gpu_max(roi_count),
host_sum(roi_count),
host_sum2(roi_count),
host_pixels(roi_count),
host_panel_v(roi_count * panel_slots),
host_panel_x(roi_count * panel_slots),
host_panel_y(roi_count * panel_slots),
host_max(roi_count),
max_init(roi_count, INT_MIN) {
// The current device, not device 0: workers are pinned round-robin across the GPUs, so device 0's
// SM count can belong to a different card than the one these kernels launch on.
int device = 0;
cuda_err(cudaGetDevice(&device));
cudaDeviceProp prop{};
cuda_err(cudaGetDeviceProperties(&prop, device));
threads = 128;
blocks = 4 * prop.multiProcessorCount;
shared_needed = roi_count * (3 * sizeof(unsigned long long) + sizeof(int))
+ roi_count * panel_slots * 3 * sizeof(unsigned long long);
std::vector<int> box;
for (const auto &m: modules.Get())
box.insert(box.end(), {static_cast<int>(m.x0), static_cast<int>(m.y0), static_cast<int>(m.width),
static_cast<int>(m.height)});
if (!box.empty()) {
gpu_panel_box = CudaDevicePtr<int>(box.size());
cuda_err(cudaMemcpyAsync(gpu_panel_box, box.data(), sizeof(int) * box.size(),
cudaMemcpyHostToDevice, *stream));
}
// On this engine's stream, like every other operation it issues: the streams are non-blocking, so a
// NULL-stream copy is no longer ordered against the kernels that read the map. The one-time
// synchronise leaves the constructor with the upload settled rather than in flight.
cuda_err(cudaMemcpyAsync(gpu_roi_map, roi_map.data(), sizeof(uint16_t) * npixel,
cudaMemcpyHostToDevice, *stream));
cuda_err(cudaStreamSynchronize(*stream));
}
void ROIIntegrationGPU::Run(const ImagePreprocessorBuffer &image, std::map<std::string, ROIMessage> &out) {
if (image.size() != npixel)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"ROIIntegration: mismatch in image size");
cuda_err(cudaMemsetAsync(gpu_sum, 0, sizeof(unsigned long long) * roi_count, *stream));
cuda_err(cudaMemsetAsync(gpu_sum2, 0, sizeof(unsigned long long) * roi_count, *stream));
cuda_err(cudaMemsetAsync(gpu_pixels, 0, sizeof(unsigned long long) * roi_count, *stream));
const size_t slots = roi_count * panel_slots;
cuda_err(cudaMemsetAsync(gpu_panel_v, 0, sizeof(unsigned long long) * slots, *stream));
cuda_err(cudaMemsetAsync(gpu_panel_x, 0, sizeof(unsigned long long) * slots, *stream));
cuda_err(cudaMemsetAsync(gpu_panel_y, 0, sizeof(unsigned long long) * slots, *stream));
cuda_err(cudaMemcpyAsync(gpu_max, max_init.data(), sizeof(int) * roi_count, cudaMemcpyHostToDevice, *stream));
gpu_roi<<<blocks, threads, shared_needed, *stream>>>(
gpu_roi_map, image.getGPUBuffer(), npixel, width, roi_count,
gpu_panel_box, static_cast<int>(modules.size()), static_cast<int>(panel_slots),
gpu_sum, gpu_sum2, gpu_pixels, gpu_panel_v, gpu_panel_x, gpu_panel_y, gpu_max);
cuda_err(cudaGetLastError());
cudaMemcpyAsync(host_sum.data(), gpu_sum, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(host_sum2.data(), gpu_sum2, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(host_pixels.data(), gpu_pixels, sizeof(unsigned long long) * roi_count, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(host_panel_v.data(), gpu_panel_v, sizeof(unsigned long long) * slots, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(host_panel_x.data(), gpu_panel_x, sizeof(unsigned long long) * slots, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(host_panel_y.data(), gpu_panel_y, sizeof(unsigned long long) * slots, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(host_max.data(), gpu_max, sizeof(int) * roi_count, cudaMemcpyDeviceToHost, *stream);
cuda_err(cudaStreamSynchronize(*stream));
for (uint16_t r = 0; r < roi_count; r++) {
roi_sum[r] = static_cast<int64_t>(host_sum[r]);
roi_sum2[r] = host_sum2[r];
roi_pixels[r] = host_pixels[r];
roi_max[r] = (host_max[r] == INT_MIN) ? INT64_MIN : static_cast<int64_t>(host_max[r]);
}
for (size_t k = 0; k < slots; k++) {
roi_panel_v[k] = static_cast<int64_t>(host_panel_v[k]);
roi_panel_x[k] = static_cast<int64_t>(host_panel_x[k]);
roi_panel_y[k] = static_cast<int64_t>(host_panel_y[k]);
}
PlaceWeighted();
Export(out);
}