leonarski_fandClaude Opus 5.5
ebce906025
Combines the stills reader and module work (stills-readers, stills-modgeom, stills-euxfel) onto rc178 with the owner's decisions for this release: - Inputs are files, never a directory; several files of one format are one dataset (the multi-input CLI of the previous commit), so every reader takes an explicit list: JFJochXFELReader::ReadFiles, ReadCXI, ReadPanelTable and JFJochXTCReader::ReadFiles take std::vector<std::string>; ListFiles and xtc::CollectStreams are gone, CanRead* accept a regular file only. - One HDF5 frame reader (JFJochCrystFELReader -> JFJochXFELReader) parameterised by what the file holds: per-shot groups or a 3D stack, a /metadata panel table (posx/posy/angle, pixel size, nominal camera length, pixel mask: as SACLA writes), a Cheetah CXI single panel (square frame; a tiled slab is refused with a message). At most 8 files open; every file checked against the first. Signed 32-bit decode, per-frame 3D masks, panels at their own coffset (from the EuXFEL work). - Frames stored one chunk each are read the way the NXmx reader reads its images: only the chunk's place is asked of HDF5 under its lock (H5Dget_chunk_info_by_coord), the bytes are read through HDF5ImageSource::RawFile (positional, no lock) and decoded outside it - deflate(+shuffle) by zlib, bitshuffle/LZ4 (and zstd, plain LZ4) by CompressedImage's decoders. Bitshuffle/LZ4 used to go through HDF5's filter under the global lock, one frame at a time. - LCLS-I XTC (Rayonix): wavelength from the beam record, pixel size from the Rayonix model and binning, only --detector-distance needed; damaged/compressed frames skipped, a truncated last event dropped; std::ifstream, no POSIX calls: builds with MSVC. No DIALS .expt support at all. - CrystFEL .geom: module geometry only (panel ranges, fs/ss, corners, pixel size, coffset, data path) and optionally the camera length; everything else is ignored with a note in the log. - --mask-good / --mask-bad <file>:<dataset>: a mask array in another HDF5 file, in the frames' stored layout (what a .geom's mask_file used to give). - Gain measured on the background for panel-table and CXI input that states none (--gain overrides). - Detector modules from explicit geometry only (DetectorModules: the reader's panels, an NXmx file with one NXdetector_module per module, or --module-geometry); never from the image. Spots and predictions are mapped through the modules, the image is not re-assembled. - Module refinement in the stills bundle adjustment (Ceres; per-module shift and in-plane turn, gauge on mean shift/turn/scale and on the two tilt-like patterns when the tilt is refined; adopted only where it predicts held-out frames better). Applied for a foreign multi-panel detector (panel table, .geom panels); for a JUNGFRAU measured and reported only. Written to <prefix>_modules.h5 (NXmx NXdetector_module groups), read back with --module-geometry. - A panel-table file's camera length is nominal: with a reference cell it is refined from the cell. - Broker and writer output unchanged: masters keep the single NXdetector_module group, the start message carries no module list. Tests: [CrystFELGeometry], JFJochXFELReader_*, JFJochXTCReader, [JFJochMultiReader], [CellPopulation], SaturationCeiling_*, [DetectorModules], RefineGlobalGeometry_ModulePlacement, [reindex], Sublattice. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
31 lines
1.7 KiB
C++
31 lines
1.7 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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#include <string>
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#include "../common/DetectorModules.h"
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#include "../common/DetectorOrientation.h"
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#include "../common/DiffractionGeometry.h"
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#include "HDF5Objects.h"
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// The detector's modules as NXmx describes them: one NXdetector_module group per module,
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// /entry/instrument/detector/module_<n>, after the NeXus base class NXdetector_module
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// (https://manual.nexusformat.org/classes/base_classes/NXdetector_module.html) as NXmx uses it
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// (https://manual.nexusformat.org/classes/applications/NXmx.html):
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// - data_origin, data_size: where the module is in the image array, slowest index first ([row, column]);
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// - module_offset: translation from the image's pixel (0, 0) to the module's first pixel, depends_on
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// the detector's own translation (the sample -> pixel (0, 0) vector the master writes);
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// - fast_pixel_direction, slow_pixel_direction: translation of one pixel along the module's columns and
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// rows, depends_on module_offset.
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// Vectors are in the McStas frame, lengths in metres. A pixel (row i, column j) of a module is then at
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// translation + module_offset + j fast + i slow - the convention dxtbx reads.
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void WriteNXmxModules(HDF5Object &file, const DetectorModules &modules, double pixel_size_m,
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const DetectorOrientation &orientation, const std::string &depends_on);
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// A file holding only the module geometry (and the detector translation it hangs from), for
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// rugnux --module-geometry.
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void WriteModuleGeometryFile(const std::string &path, const DetectorModules &modules,
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const DiffractionGeometry &geom);
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