leonarski_f
a395f358ef
* Rugnux: Performance improvements on GPU and CPU (more of the pre-scan and of scaling on the GPU, faster CPU spot finding and crystal refinement), with unchanged results. * Rugnux: More robust processing - patches of persistently hot pixels are masked, an inconsistent merge triggers a retry at the measured beam centre, and builds targeting different CPU levels give the same results. * Rugnux: Improved scaling and merging - reflections with an overloaded pixel are dropped, as in XDS, sparse rotation sweeps are scaled more reliably, and French-Wilson amplitudes use an anisotropic Wilson prior. * Rugnux: Improved space-group determination - glide planes in groups without a centre of symmetry, screw axes from short or weak axial rows kept when a higher group is adopted, and more reliable decisions on twinned and pseudo-symmetric crystals. * Rugnux: Improved small-molecule processing - spots that grow wider than the integration disk and split spots are integrated over their measured footprint, sparse lattices are integrated on every frame, and the `.hkl` file holds unmerged scaled reflections (SHELX HKLF 4). * Rugnux: Reads Rigaku d*TREK SMV images (Saturn CCD), including detector 2theta and encoded pixel overflows; home-source (rotating-anode) datasets were added to the validation battery. * jfjoch_viewer: Fixed processing failing at the end with "Wrong JPEG library version" on Linux; the merge window shows the space group with proper subscripts and a checklist of crystal pathologies. Reviewed-on: #84 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
13 KiB
Third-party software notices
Jungfraujoch is licensed under GPL-3.0 (see LICENSE); the FPGA design is
licensed under CERN-OHL-S-2.0 (see fpga/LICENSE). It builds on a number of
third-party components, acknowledged below as required by their licenses.
This file is the human-readable manifest. The verbatim license texts live in the
licenses/ directory (regenerate with bash licenses/COLLECT.sh). The frontend's
bundled JavaScript dependencies are listed separately in
frontend/dist/THIRD_PARTY_LICENSES.txt, generated at build time (npm run licenses).
All licenses below are GPL-3.0-compatible, with one exception: the NVIDIA CUDA Toolkit is used under its own EULA (see the notes at the end of this file).
Fetched at build time and statically linked into the C++ binaries
These are downloaded by CMake (FetchContent / ExternalProject) during the first configure and
linked into the Jungfraujoch executables.
| Component | Version | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| spdlog | 1.17.0 | Gabi Melman | MIT | spdlog.txt |
| Zstandard | 1.5.7 | Meta Platforms, Inc. | BSD-3-Clause | zstd.txt |
| HDF5 | 2.2.0 | The HDF Group; UIUC | BSD-3-Clause-style + Apache-2.0 | hdf5.txt |
| slsDetectorPackage | 8.0.2 / 9.2.0 | PSI | LGPL-3.0-or-later | LGPL, GPL |
| cpp-httplib | 0.56.0 | Yuji Hirose | MIT | cpp-httplib.txt |
| libzmq (ZeroMQ) | 4.3.5 | iMatix and contributors | MPL-2.0 | libzmq.txt |
| libtiff | 4.7.2 | Sam Leffler; SGI | libtiff (BSD-like) | libtiff.txt |
| FFTW | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | fftw.txt |
| Ceres Solver | (pinned) | Google Inc. and contributors | BSD-3-Clause | ceres-solver.txt |
| Abseil | 20250127 (required by Ceres) | Google Inc. | Apache-2.0 | abseil.txt |
| fast-feedback-indexer | (pinned) | PSI | BSD-3-Clause | fast-feedback-indexer.txt |
| libjpeg-turbo | 3.2.0 | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | libjpeg-turbo.txt |
| curl | 8.22.0 | Daniel Stenberg and contributors | curl (MIT-like) | curl.txt |
| Catch2 | 3.16.0 | Catch2 Authors | BSL-1.0 | catch2.txt |
| zlib-ng | 2.3.3 | Jean-loup Gailly and Mark Adler; the zlib-ng contributors | Zlib | zlib.txt |
| Eigen | 3.4.1 | Benoit Jacob, Gael Guennebaud and contributors | MPL-2.0 (+ BSD parts) | eigen.txt, README |
libcurl is fetched and statically linked only for viewer builds (JFJOCH_VIEWER_BUILD /
JFJOCH_VIEWER_ONLY), where it is jfjoch_viewer's HTTP client; the broker and writer never link
it. Its TLS and Kerberos backends are the OS-native ones (Schannel/SSPI on Windows, OpenSSL and
system krb5 on Linux), so no TLS stack is vendored with it.
Catch2 is used only to build the test binary (jfjoch_test) and is not part of any shipped
artifact; it is listed here for completeness.
zlib is supplied by zlib-ng built in its zlib-compatible mode (same zlib.h, same API and symbol
names), so it is the zlib that HDF5, libtiff, cpp-httplib, libcurl and GEMMI all link. It is
built during the configure rather than added as a subproject; the licence is the zlib licence
either way. Eigen is header-only: only its headers reach the binaries, and no Eigen CMake runs.
Vendored directly in the repository
These live in the source tree (see the path) rather than being fetched; traccc and the Ceres-derived minimiser are the exceptions - code adapted into first-party files rather than a vendored directory, see the notes at the end of this file.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| nlohmann/json | include/nlohmann/ |
Niels Lohmann | MIT | nlohmann-json.txt |
| Macaron Base64 | include/base64/ |
tomykaira | MIT | base64-macaron.txt |
| TinyCBOR | frame_serialize/tinycbor/ |
Intel Corporation | MIT | tinycbor.txt |
| Bitshuffle | compression/bitshuffle/ |
Kiyoshi Masui | MIT | bitshuffle.txt |
| Bitshuffle (h-perf) | compression/bitshuffle_hperf/ |
Kal Conley | Apache-2.0 | bitshuffle-hperf.txt |
| LZ4 | compression/lz4/ |
Yann Collet | BSD-2-Clause | lz4.txt |
| HLS arbitrary-precision types | fpga/include/ |
Xilinx, Inc. | Apache-2.0 | xilinx-hls-headers.txt |
| GEMMI | gemmi_gph/ |
Global Phasing Ltd. | MPL-2.0 | gemmi.txt |
| PEGTL | gemmi_gph/gemmi/third_party/tao/ |
Dr. Colin Hirsch and Daniel Frey | MIT | pegtl.txt |
| sajson | gemmi_gph/gemmi/third_party/sajson.h |
Chad Austin | MIT | sajson.txt |
| fast_float | gemmi_gph/gemmi/third_party/fast_float.h |
The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | fast-float.txt |
| half | gemmi_gph/gemmi/third_party/half.hpp |
Christian Rau | MIT | half.txt |
| pocketfft | gemmi_gph/gemmi/third_party/pocketfft_hdronly.h |
Max-Planck-Society; Peter Bell; MIT (FFTW-derived parts) | BSD-3-Clause | pocketfft.txt |
| tinydir | gemmi_gph/gemmi/third_party/tinydir.h |
Cong Xu, Lautis Sun, Baudouin Feildel, Andargor | BSD-2-Clause | tinydir.txt |
| traccc (ACTS) | image_analysis/spot_finding/StrongPixelSet.cpp, SpotExtractorGPU.cu |
CERN, for the benefit of the ACTS project | MPL-2.0 | traccc.txt |
| Ceres Solver (adapted) | image_analysis/geom_refinement/LMSolver.h, LMSolver.cpp |
Google Inc. | BSD-3-Clause | ceres-solver.txt |
| xbflash.qspi | tools/xbflash.qspi/ |
Xilinx / AMD | Apache-2.0 | xbflash-qspi.txt |
| wingetopt | tools/wingetopt/ |
Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | wingetopt.txt |
Runtime libraries and SDKs (shipped in binaries, not in the source tree)
| Component | Used by | License | Notice |
|---|---|---|---|
| Qt 6 | jfjoch_viewer |
LGPL-3.0 | notice, LGPL-3.0 |
| NVIDIA CUDA Toolkit (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | notice, EULA |
Frontend (npm) dependencies
The React/TypeScript frontend (frontend/) bundles a large transitive tree of npm packages,
overwhelmingly MIT/ISC/BSD/Apache-2.0 licensed. Their full notices are generated automatically:
cd frontend && npm run licenses # writes dist/THIRD_PARTY_LICENSES.txt
The generated file is produced as part of the frontend build target and installed alongside the
served frontend, so the shipped web UI carries its own attribution.
Notes on weak-copyleft and attribution-sensitive components
- MPL-2.0 (Eigen, GEMMI, libzmq, traccc): file-level copyleft. GEMMI is vendored in
gemmi_gph/in trimmed form; libzmq and Eigen are fetched at build time (Eigen is header-only). The corresponding source is available from each project upstream. - GEMMI's own bundled third-party headers — PEGTL, sajson, fast_float, half, pocketfft and
tinydir, all under
gemmi_gph/gemmi/third_party/— are listed separately above rather than being absorbed into GEMMI's row: they are other authors' code under other licences (MIT, BSD and Apache/MIT/BSL), and GEMMI's MPL-2.0 does not speak for them. Their terms are carried in the headers themselves rather than inLICENSEfiles, so thelicenses/*.txtcopies are kept by hand; only PEGTL ships aLICENSE, whichCOLLECT.shcopies. - traccc is the one entry that is not a vendored directory. Its sparse connected-component
labelling enters two otherwise first-party files:
StrongPixelSet.cppadapts the SparseCCL source, andSpotExtractorGPU.cufollows the design of its GPU counterpart. MPL-2.0 is file-level, so both files name the origin at the top and are covered bylicenses/traccc.txt. See ACKNOWLEDGEMENT.md for the citation. - Ceres Solver is also fetched and linked (table above); separately,
LMSolver.h/.cppre-implement its trust-region Levenberg-Marquardt minimiser, projected line search, polynomial step choice and sphere manifold for the crystal refinement, following its source. Both files name the origin at the top and are covered bylicenses/ceres-solver.txt. - FFTW is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
- Apache-2.0 components: where upstream ships a
NOTICEfile, it is reproduced in the correspondinglicenses/text. - Qt (LGPL-3.0) and NVIDIA CUDA (EULA) carry redistribution conditions beyond a copyright
notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
(
licenses/Qt6-LGPL-3.0.txt,licenses/NVIDIA-CUDA-EULA.txt); the CUDA EULA is the one shipped with CUDA Toolkit 12.8 — replace it if you build against a different toolkit version.