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
78 lines
3.1 KiB
C++
78 lines
3.1 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 <cstdint>
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#include <optional>
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#include <string>
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#include <vector>
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// Where the panels of a stills detector lie and what their pixels are worth, as the XFEL readers
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// gather it from a file's own metadata (or, while it is still read, a CrystFEL geometry file): the
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// panels with their pixel ranges in the stored frame, fast/slow-scan directions and corners, the camera
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// length, the pixel size, the gain and the regions to leave out. The conventions are CrystFEL's - a
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// corner is the very corner of the panel's first pixel, x and y in pixels in the detector plane.
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//
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// Lengths are in pixels, except the camera length, which is held in metres. A value taken from the
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// image files (a camera length or photon energy stated per shot) is kept as its path, with the factor
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// that turns the stored number into the unit held here.
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namespace xfel {
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// A number stated in the layout, or a path to it in the image file, times scale.
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struct Value {
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std::string path; // empty: value holds the number
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double value = 0;
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double scale = 1; // what one stored unit at path is worth
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};
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struct Panel {
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std::string name;
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int64_t min_fs = 0, max_fs = 0, min_ss = 0, max_ss = 0; // inclusive, in the stored frame
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double fs_x = 1, fs_y = 0, ss_x = 0, ss_y = 1;
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double corner_x = 0, corner_y = 0;
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double res = 0; // pixels per metre
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std::optional<Value> clen; // metres
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double coffset = 0; // metres
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std::optional<double> adu_per_eV;
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std::optional<double> adu_per_photon;
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std::optional<double> max_adu;
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int64_t mask_edge_pixels = 0;
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bool no_index = false;
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};
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// A region to leave out: either a pixel range on one panel (or, in the old syntax, on the whole
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// frame), or a box in the laboratory plane, in pixels.
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struct BadRegion {
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std::string panel; // empty: fs/ss are whole-frame coordinates
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bool in_lab = false;
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double min_x = 0, max_x = 0, min_y = 0, max_y = 0;
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int64_t min_fs = 0, max_fs = 0, min_ss = 0, max_ss = 0;
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};
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// A mask array: a pixel is bad where it has any of bad's bits set, or lacks any of good's - or, with
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// nonzero_good, where the array is zero.
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struct Mask {
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std::string data; // HDF5 path
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std::string file; // file holding it, or empty for the image file itself
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uint32_t good = 0, bad = 0;
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bool nonzero_good = false;
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[[nodiscard]] bool Bad(uint32_t v) const {
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return (bad != 0 && (v & bad) != 0) || (good != 0 && (v & good) != good) || (nonzero_good && v == 0);
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}
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};
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struct Layout {
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std::vector<Panel> panels;
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std::vector<BadRegion> bad;
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std::vector<Mask> masks;
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std::string data = "/data/data";
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std::optional<Value> photon_energy; // eV
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std::optional<Value> wavelength; // Angstrom; used where no photon_energy is stated
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// A stored value below, above or at these marks a pixel unusable in that frame.
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std::optional<double> flag_lessthan, flag_morethan, flag_equal;
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};
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} // namespace xfel
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