leonarski_fandjungfrau
4dc2534dbf
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 18m57s
Build Packages / Unit tests (push) Skipped
Build Packages / build:windows:nocuda (push) Successful in 16m55s
Build Packages / build:windows:cuda (push) Successful in 18m48s
Build Packages / build:viewer-tgz:cpu (push) Successful in 13m10s
Build Packages / build:viewer-tgz:cuda (push) Successful in 14m45s
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 22m23s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 20m12s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 23m7s
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 20m43s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 23m9s
Build Packages / XDS test (durin plugin) (push) Successful in 12m26s
Build Packages / build:rpm (rocky9) (push) Successful in 24m58s
Build Packages / Generate python client (push) Successful in 50s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 23m20s
Build Packages / Create release (push) Skipped
Build Packages / XDS test (JFJoch plugin) (push) Successful in 12m37s
Build Packages / build:rpm (rocky8) (push) Successful in 27m58s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 25m38s
Build Packages / Build documentation (push) Successful in 59s
Build Packages / DIALS test (push) Successful in 23m16s
Build Packages / XDS test (neggia plugin) (push) Successful in 6m38s
**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>
88 lines
3.1 KiB
C++
88 lines
3.1 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
|
|
// SPDX-License-Identifier: GPL-3.0-only
|
|
|
|
#pragma once
|
|
|
|
#include <vector>
|
|
#include <unordered_set>
|
|
#include <map>
|
|
#include <mutex>
|
|
#include <optional>
|
|
|
|
#include "../common/TopPixels.h"
|
|
#include "JFJochReaderDataset.h"
|
|
#include "../common/CrystalLattice.h"
|
|
#include "../common/Histogram.h"
|
|
|
|
// Markers stored in place of an intensity. They occupy the bottom of the int32 range and
|
|
// INT32_MAX at the top, so anything in between is a real count. Add a marker at the BOTTOM and move
|
|
// MIN_REAL_PXL_VALUE with it - several places classify a pixel by range rather than by equality,
|
|
// and they all test against MIN_REAL_PXL_VALUE.
|
|
constexpr static int32_t ERROR_PXL_VALUE = INT32_MIN;
|
|
constexpr static int32_t GAP_PXL_VALUE = INT32_MIN + 1;
|
|
constexpr static int32_t BEAM_STOP_PXL_VALUE = INT32_MIN + 2;
|
|
constexpr static int32_t MIN_REAL_PXL_VALUE = INT32_MIN + 3;
|
|
constexpr static int32_t SATURATED_PXL_VALUE = INT32_MAX;
|
|
|
|
struct JFJochReaderRawImage {
|
|
RawByteBuffer image_buffer;
|
|
CompressedImage image;
|
|
};
|
|
|
|
class JFJochReaderImage {
|
|
std::shared_ptr<const JFJochReaderDataset> dataset;
|
|
|
|
std::vector<int32_t> image; // Image in the reader must be 32-bit signed, uncompressed
|
|
DataMessage message;
|
|
|
|
std::unordered_set<int64_t> saturated_pixel;
|
|
std::unordered_set<int64_t> error_pixel;
|
|
std::vector<std::pair<int32_t, int32_t>> valid_pixel;
|
|
|
|
// Fast stats without storing/sorting all valid pixels
|
|
int32_t valid_min = 0;
|
|
int32_t valid_max = 0;
|
|
size_t valid_count = 0;
|
|
bool has_valid = false;
|
|
|
|
// For overlay: track top pixels with a tiny O(K) structure; export to vector for UI
|
|
TopPixels top_pixels_acc{20};
|
|
std::vector<std::pair<int32_t, int32_t>> top_pixels;
|
|
|
|
// This histogram operates in square root of count from 0 to 10^20
|
|
Histogram count_histogram{100000};
|
|
|
|
constexpr static float auto_foreground_range = 99.0f;
|
|
int32_t auto_foreground;
|
|
void CalcAutoContrast();
|
|
|
|
template <class T>
|
|
void ProcessInputImage(const void* image, size_t npixel, int64_t sat_value, int64_t special_value);
|
|
void ProcessInputImage(const CompressedImage& image);
|
|
public:
|
|
JFJochReaderImage(const DataMessage &msg, const std::shared_ptr<const JFJochReaderDataset> &dataset);
|
|
JFJochReaderImage(const JFJochReaderImage &other);
|
|
|
|
const DataMessage &ImageData() const;
|
|
DataMessage &ImageData();
|
|
|
|
const std::vector<int32_t> &Image() const;
|
|
const std::unordered_set<int64_t> &SaturatedPixels() const;
|
|
const std::unordered_set<int64_t> &ErrorPixels() const;
|
|
const JFJochReaderDataset &Dataset() const;
|
|
|
|
std::optional<std::pair<int32_t, int32_t>> ValidMinMax() const;
|
|
const std::vector<std::pair<int32_t, int32_t>> &GetTopPixels() const;
|
|
|
|
void AddImage(const JFJochReaderImage& other);
|
|
std::vector<float> GetAzInt1D() const;
|
|
std::vector<float> GetAzInt1D_BinToQ() const;
|
|
std::shared_ptr<JFJochReaderDataset> CreateMutableDataset();
|
|
|
|
int32_t GetAutoContrastValue() const;
|
|
|
|
std::vector<float> GetHistogram() const;
|
|
};
|
|
|
|
|