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Jungfraujoch/licenses/COLLECT.sh
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leonarski_f 538f3504d3
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v1.0.0.rc-161 (#71)
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.

* **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice.
* **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster.
* **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory.
* **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again.

**Breaking change to the rugnux command line:**
* `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one.
* `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride.

**Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional:
* `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve.
* `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing.

**Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional:
* The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more.
* `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.**

Reviewed-on: #71
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-13 17:03:10 +02:00

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#!/usr/bin/env bash
# Collect the verbatim license texts of all third-party components into this directory.
#
# This is the bulk reference material that accompanies THIRD_PARTY_NOTICES.md (the human-readable
# manifest at the repo root). Run from the repo root after a configure/build has populated the
# FetchContent source trees (build/_deps or cmake-build-*/_deps). Re-run when a dependency version
# changes. The output (licenses/*.txt) is committed so a source checkout needs no build to ship the
# notices.
#
# bash licenses/COLLECT.sh
#
set -euo pipefail
cd "$(dirname "$0")/.."
OUT=licenses
# Copy $1 to licenses/$2, trying each source path in $1 (space-separated) until one exists.
copy_license() {
local dest="$1"; shift
local src
for src in "$@"; do
if [[ -f "$src" ]]; then
cp "$src" "$OUT/$dest"
echo " $dest <- $src"
return 0
fi
done
echo " !! MISSING: $dest (none of: $*)" >&2
return 0
}
# Search the populated dependency trees in order of preference.
DEPS=(_deps cmake-build-release/_deps build/_deps cmake-build-debug/_deps)
find_dep() { # find_dep <relative-path-under-a-deps-dir>
local d
for d in "${DEPS[@]}"; do [[ -f "$d/$1" ]] && { echo "$d/$1"; return; }; done
}
echo "Collecting third-party license texts into $OUT/ ..."
# --- Fetched at build, statically linked into the C++ binaries -------------------------------
copy_license spdlog.txt "$(find_dep spdlog-src/LICENSE)"
copy_license zstd.txt "$(find_dep zstd-src/LICENSE)"
copy_license hdf5.txt "$(find_dep hdf5-src/LICENSE)"
copy_license catch2.txt "$(find_dep catch2-src/LICENSE.txt)"
copy_license cpp-httplib.txt "$(find_dep httplib-src/LICENSE)"
copy_license libzmq.txt "$(find_dep libzmq-src/LICENSE)"
copy_license libtiff.txt "$(find_dep tiff-src/LICENSE.md)"
copy_license fftw.txt "$(find_dep fftw-src/COPYING)"
copy_license ceres-solver.txt "$(find_dep ceres-src/LICENSE)"
copy_license fast-feedback-indexer.txt "$(find_dep fast-indexer-src/LICENSE.md)"
copy_license eigen.txt "$(find_dep eigen3-src/COPYING.MPL2)"
copy_license eigen-README.txt "$(find_dep eigen3-src/COPYING.README)"
copy_license zlib.txt "$(find_dep zlib-src/LICENSE.md)"
# slsDetectorPackage is LGPL-3.0-or-later: ship both the GPL-3.0 base and the LGPL-3.0 addendum.
copy_license slsDetectorPackage-LGPL-3.0.txt "$(find_dep sls_detector_package-src/LICENSES/LGPL-3.0)"
copy_license slsDetectorPackage-GPL-3.0.txt "$(find_dep sls_detector_package-src/LICENSES/GPL-3.0)"
# libjpeg-turbo is built out-of-line by preview/ (ExternalProject), not under _deps.
copy_license libjpeg-turbo.txt \
cmake-build-release/preview/libjpeg-turbo/src/libjpeg-turbo-project/LICENSE.md \
build/preview/libjpeg-turbo/src/libjpeg-turbo-project/LICENSE.md
# --- Vendored directly in the repository ----------------------------------------------------
copy_license nlohmann-json.txt include/nlohmann/LICENSE.MIT
copy_license tinycbor.txt frame_serialize/tinycbor/LICENSE
copy_license bitshuffle.txt compression/bitshuffle/LICENSE
copy_license bitshuffle-hperf.txt compression/bitshuffle_hperf/LICENSE-APACHE
copy_license lz4.txt compression/lz4/LICENSE
copy_license xilinx-hls-headers.txt fpga/include/LICENSE.HLS_Headers
copy_license gemmi.txt gemmi_gph/LICENSE.txt
copy_license xbflash-qspi.txt tools/xbflash.qspi/LICENSE
copy_license wingetopt.txt tools/wingetopt/LICENSE
# --- Runtime SDK license texts, copied from their system install (best effort) ---------------
# These come from outside the build tree; the committed copies are authoritative if absent here.
copy_license Qt6-LGPL-3.0.txt /usr/share/common-licenses/LGPL-3
copy_license NVIDIA-CUDA-EULA.txt \
/usr/local/cuda/EULA.txt /usr/local/cuda-12.8/EULA.txt
echo "Done. base64-macaron.txt, traccc.txt, Qt6-NOTICE.txt and NVIDIA-CUDA-NOTICE.txt are maintained by hand."