f5a990dc8dd65bcceec4d8a77dd3a2de60f5d7da
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Commits
| Author | SHA1 | Message | Date | |
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  leonarski_fandClaude Opus 5.5
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d345deaecd |
XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel
On a deflated Cheetah CXI with a per-frame mask (AGIPD 1M), half of the reader's time after the inflate went to turning the stored frame into the image: the mask plane widened into a zeroed uint32 copy before being tested, MarkBad testing it with a branch per pixel through a reference the store could alias, and the photon conversion calling lroundf and branching on the mask, the finiteness and the clamp. Now the mask is tested as stored (uint16 or uint32), and both loops are written so that the compiler vectorises them: std::lround spelled out exactly (truncate, the exact fraction, a half or more away from zero) and the selects done as arithmetic (Pick). Plain C++, no intrinsics. Bit-identical: FNV hash of every image handed out (2000 frames) plus the pixel mask, before and after, on a CXI with a CrystFEL geometry (with and without a gain), a panel-table HDF5 (with and without a gain) and a bitshuffle/LZ4 int16 set: all identical. Reader alone, one thread: 14.1 -> 7.0 ms per frame. rugnux on the 14,445-frame CXI run (16 workers, A/B back to back): geometry refinement sample 11.4 -> 8.9 s, image pass 27.6 -> 21.1 s, whole run 67.4 -> 58.2 s; geometry and refinement log lines identical. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu |
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leonarski_fandClaude Opus 5.5
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7c23b4befe |
CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them
The .geom parser now takes the masking information the format defines: - mask arrays: mask/mask_file/mask_good/mask_bad (mask 0) and maskN_data/maskN_file/maskN_goodbits/ maskN_badbits for N = 0..7; global keys hold for the panels after them, a panel may override. A mask that is the same on every panel is one whole-frame mask, otherwise one per panel, applied on that panel's pixels only. - a relative mask_file is looked for in the working directory (as CrystFEL does), then beside the .geom. - bad regions (bad*): a lab-plane box (min_x..max_y) or a fs/ss range on a panel (or, old syntax, on the whole frame); mask_edge_pixels and no_index. JFJochXFELReader already had the static pixel mask and the per-frame mask path for these; the masks go through them unchanged. A mask whose path holds % (one per shot group) is applied frame by frame like a 3D one. Where the geometry names mask arrays, the data file's own Cheetah masks (CXI mask_shared and per-shot mask with Cheetah's generic bad bits, /metadata/pixelmask) are not added: the geometry says which bits matter (e.g. an AGIPD mask_bad that includes bit 32). --mask-good / --mask-bad still add their masks to these. Tests: [CrystFELGeometry] (new keys, per-panel override, relative mask file), JFJochXFELReader_* (new GeometryMasks case on a synthetic CXI + .geom), [JFJochMultiReader], JFJochXTCReader*. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu |
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leonarski_fandClaude Opus 5.5
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95e51f868d |
XFEL reader: integer frames stay integer, one gain, placement by panel
DecodeInto no longer turns every stored pixel into a float and back:
- the gain is one value (adu_per_photon_), not a float per stored pixel
- it always was one value; only --gain or a measured gain set it;
- a 16-bit signed frame (Cheetah CXI, SACLA) without a gain is handed
up as Int16, in its own type; other integer frames are widened to
int32 without a float; only a float frame or a gain other than one
goes through lround(v / gain), exactly as before;
- placement is per panel (start, size, destination steps) instead of a
64-bit destination per stored pixel; a panel square with the image
is copied row by row (PAL: 1440x1440 into 1444x1444 - the two-pixel
margin is Place()'s, kept so the geometry does not move);
- the decode buffers (chunk, inflated, unshuffled) are reused per
thread, the bitshuffle decode is not copied again;
- a chunk whose HDF5 filter_mask is not zero (a filter skipped) is
read by HDF5 instead of being decoded as if it were not;
- the never-set value flags (flag_lessthan/morethan/equal) are gone
from the layout and from the per-pixel loop.
MeasureGain in the CLI now reads Int16 frames as well, so a SACLA run
still has its gain measured.
Tests: JFJochXFELReader_SACLA/_CXI updated for the mode, new
JFJochXFELReader_CXI_Int16 (deflate without shuffle, a chunk with its
filter skipped) and JFJochXTCReader_StoredPixels (synthetic XTC,
stored hand-up and the offset path).
Measured on two PAL-XFEL Rayonix sets (int16, deflate; RTX 5080,
5950X, page cache warm; reports and .hkl identical to the baseline):
main pass, 2000 frames: 296 -> 799 frames/s (pal86),
302 -> 755 frames/s (pal90)
wall, 2000 frames: 26.4 -> 13.6 s, 32.1 -> 19.4 s
(the geometry-refinement steps, which read frames too, halve)
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
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leonarski_fandClaude Opus 5.5
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ebce906025 |
Serial XFEL stills inputs: readers from the files themselves, module geometry and its refinement
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 |