9 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	dfd69fcb91	marCCD frames are widened on the device ... The marCCD reader read each frame's 16-bit scanlines into scratch and widened them to int32 on the worker thread (marccd::ReadInto, ~20 % of the image-loop worker CPU on 4nwv), and the 4-byte image was uploaded. ReadRawImage now reads the scanlines straight into the image's buffer and hands them over as a new read-only CompressionAlgorithm::UINT16_WIDENED (mode Int32): two bytes a pixel cross PCIe, from page-locked memory, and the preprocessing kernel widens them itself. It is not CompressedImageMode::Uint16, which calls 65535 an error pixel; a marCCD's 65535 is its saturation marker. So the kernel compares each pixel with int32's error marker and the int32 saturation cap - the comparisons are made on the pixel's value, in int64, rather than in the storage type - and decides every pixel exactly as for the int32 image the host would have widened it to. The host widening (JFJochDecompressPtr) is the CPU path. Test: ImagePreprocessorGPU_StoredEncodingsMatchCPU, with a frame carrying 65535 at a saturation of 65535, against the CPU preprocessor on the host-widened image. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3	2026-10-12 22:37:47 +02:00
leonarski_fandClaude Opus 5.5	f4252ad39d	miniCBF frames are decoded on the device ... The CBF reader decoded every frame's x-CBF_BYTE_OFFSET stream on the worker thread - 19-30 % of the image-loop worker CPU on CBF sets (7qij, 4mtk) - and the 4-byte image was then uploaded. ReadRawImage now hands over the stream as the file stores it, in the image's own buffer, as a new read-only CompressionAlgorithm::CBF_BYTE_OFFSET (mode Int32, what it decodes to), and ImagePreprocessorGPU decodes it on the card into the same int32 image and runs the same preprocessing kernel on it. The device decode (CBFDecoderGPU) cuts the stream into 256-byte tiles. A token is 1, 3, 7 or 15 bytes, so a tile can be entered at 15 offsets; for each one thread works out where the decode leaves the tile, how many pixels it emitted and their sum modulo 2^32 (the walks from different entries meet within a few bytes, after which they are one walk). An exclusive scan composing these maps gives each tile its true entry, first pixel and running value, and a second walk writes the pixels. A stream that ends before the image is refused as on the host. The host decoder moves to compression/ (DecodeCBFByteOffset) and is reached through JFJochDecompressPtr, so every host consumer - the CPU build, the azimuthal-integration worker, the pre-scan's shadow and gain passes - decodes exactly as before, now from the stream. It is the CPU path, not a fallback: a frame the device refuses is not retried on the host. A process file written from CBF input stores the decoded int32 image, as it always did. .cbf.gz is still inflated on the host. Tests: CBFDecoderGPU_MatchesHost (every token size, 0x80 inside payloads, escape runs across tiles, trailing CIF text), CBFDecoderGPU_ShortStreamIsRefused, ImagePreprocessorGPU_StoredEncodingsMatchCPU. Checked locally against the host decoder on 36 real frames of 9 open-arm CBF sets (signed 32-bit, signed and unsigned 16-bit, plain and gzip): identical. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3	2026-10-12 22:37:37 +02:00
leonarski_f	680c36c20d	v1.0.0-rc.166 (#76) ... * `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-02 21:17:31 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00
leonarski_f	cc3eb8352c	v1.0.0-rc.148 (#58) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_broker: Improve azimuthal integration (add <I^2> calculation) * jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated) * jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin Reviewed-on: #58	2026-06-08 08:30:35 +02:00
leonarski_f	28d224afab	version 1.0.0-rc.25	2024-11-22 21:25:20 +01:00
leonarski_f	bef9f440ce	CompressionAlgorithm: Make BSHUF_LZ4 default	2023-11-16 19:59:33 +01:00
leonarski_f	16bbf54f2a	Remove open source license (for now)	2023-09-15 10:47:21 +02:00
leonarski_f	1757d42182	Initial commit ... Signed-off-by: Filip Leonarski <filip.leonarski@psi.ch>	2023-04-06 11:17:59 +02:00