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leonarski_fandClaude Opus 5	fd9e7bce1f	CI: drive the Windows rugnux build from cmd, as the viewer build already does ... The job used shell: bash, and the Windows runner has no bash on PATH, so it failed before running cmake. It also skipped the MSVC environment, which every cmake invocation on that runner needs: build-windows calls vcvars64.bat, located through vswhere, at the start of each step. Follow it exactly - cmd, the same vcvars preamble, -G Ninja, and cpack from inside the build directory - and keep powershell only for the upload, which is what build-windows uses there too. CMAKE_PREFIX_PATH drops the Qt entry and keeps C:/deps: JFJOCH_RUGNUX_ONLY is the portable subtree minus viewer/, so it needs Eigen and ZLIB and no Qt. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 20:12:55 +02:00
leonarski_fandClaude Opus 5	6a7404f03f	CI: upload the rugnux artifacts the way every other job does ... The three new rugnux jobs reached for akkuman/gitea-release-action@v1, which does not exist on this Gitea: actions resolve against gitea.psi.ch/<owner>/<repo>, so the runner tried to clone gitea.psi.ch/akkuman/gitea-release-action and failed. That happens while preparing the workflow, before any step runs, so all three jobs died immediately without building anything. Every other job uploads with gitea_upload_file.py and the release token, so use that: bash on the Linux jobs, powershell on the Windows one, matching the viewer tarball and installer steps they sit next to. The Linux archives are renamed .tar.gz -> .tgz first, as the viewer archive already is. actions/checkout is now the only external action the workflow references. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 20:09:50 +02:00
leonarski_fandClaude Opus 5	8d32024dd1	Ship jfjoch_viewer and rugnux as two packages, and cross-build rugnux for arm64 ... The viewer tarball also carried rugnux, jfjoch_extract_hkl and jfjoch_recompress. A GUI download that contains a batch processor is confusing on its own, and it forced anyone who only wanted rugnux to take Qt with it. JFJOCH_RUGNUX_ONLY is the viewer-only subtree minus viewer/ and tools/, so it needs no Qt at all, and each of the two options now yields one artifact holding one program: JFJOCH_VIEWER_ONLY jfjoch_viewer .tar.gz / installer / .dmg JFJOCH_RUGNUX_ONLY rugnux .tar.gz / .zip The two CLI tools are still built and no longer installed anywhere. rugnux gets a CPack component of its own, so its notices land in share/doc/jfjoch_rugnux. What makes the split possible is linking cuFFT statically in both products. It was the only CUDA component still dynamic - cudart and the fast-feedback indexer were already static - and shipping it as a .so meant each self-contained archive had to carry the library beside its executables and find it again through an $ORIGIN rpath. That rpath was set on jfjoch_viewer alone, while the same tarball installed three more executables, so those shipped with no runpath at all (cmake strips the build-tree one, which points at the build host's CUDA directory) and could not load the libcufft lying next to them. Static, an artifact is one file that runs: the x86_64 rugnux tarball needs only libc, libstdc++, libgcc_s, libm, libpthread, librt and libdl. The bundling code and the rpath both go away. libcufft_static.a carries a relocatable-device-code object, so a consuming executable needs a CUDA device link; CUDA 13 no longer ships the libcufft_static_nocallback.a that used to avoid this. CUDA_RESOLVE_DEVICE_SYMBOLS emits that step while leaving the host link driver alone, so the -march and -flto flags CI passes still apply. The server build keeps the shared library: its .deb/.rpm take CUDA from the distro, and every executable there would otherwise need the same device link. The guards that exclude server-side targets keyed on NOT JFJOCH_VIEWER_ONLY, which a rugnux-only build does not satisfy - it failed on jfjoch_writer pulling in JFJochImagePuller. They now key on JFJOCH_PORTABLE_ONLY, true for either product, rather than on one product's option in five places. docker/ubuntu2404 additionally cross-compiles rugnux for arm64 SBSA, which is both DGX Spark (GB10, sm_121) and Grace Hopper (GH200, sm_90); one binary with both fatbins runs on either. It needed three things beyond a cross gcc. arm64 is published on ports.ubuntu.com and Noble's deb822 sources carry no Architectures: field, so adding the architecture without splitting the entries 404s on every index. The CUDA cross packages are in neither the x86_64 repo nor the sbsa one but in cross-linux-sbsa, whose fatbinary_section.h ships only in the x86_64 target tree even though it is architecture-neutral. And HDF5 has two try_run probes, so qemu-user-static is needed as CMAKE_CROSSCOMPILING_EMULATOR; every other fetched dependency either guards its run-checks or has none. The cross-built tarball is one ELF aarch64 binary carrying all 17 GPU modules for both sm_90 and sm_121, needing no cuFFT and no CUDA runtime at run time. It is untested on hardware: XDS is x86-64 only, so CI can show it links but only a Spark or a GH200 can show it works. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 19:23:59 +02:00
leonarski_fandClaude Opus 5	46ed703eca	libjpeg-turbo: follow the parent build's toolchain when cross-compiling ... libjpeg-turbo is brought in with ExternalProject_Add rather than FetchContent, because upstream does not support inclusion via add_subdirectory. An ExternalProject is a separate cmake invocation that inherits nothing from its parent, and the CMAKE_CACHE_ARGS here named only the feature options, so it always configured for the build host. That is invisible in a native build and fatal in a cross build: the library compiles for x86_64 inside an aarch64 build and the mistake only surfaces at the final link of whatever consumes it, as an architecture mismatch on libjpeg.a rather than anything pointing at this file. rugnux reaches it through JFJochWriter -> JFJochPreview, so it is on the path of every build, not just the viewer's. Forward the toolchain file and the compiler. CMAKE_TOOLCHAIN_FILE is empty in a native build and cmake ignores it there, so nothing changes off the cross path. libjpeg-turbo selects its own SIMD from the target architecture, so this also gets the NEON kernels for free on aarch64 and stops nasm from being consulted at all; a cross-compiled libjpeg.a comes out ELF aarch64 with 14 NEON objects. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 19:20:43 +02:00
leonarski_fandClaude Opus 5	3ea1206775	Space-group search: raise the twin-law H bound from 1.70 to 1.85 ... Re-measured over ~780 reports - three batteries and four de-novo integration-radius arms - H is the only Stage-A guard that ever fires: 14 refusals on three crystals, and not one chi-squared-ratio refusal or b veto anywhere. Two of the three are the genuine trigonal twins, reading 1.90 and 1.91 on every arm and 3.61-4.80. The third is a weak tetragonal crystal reading 1.73-1.80 that is not twinned: its 422 is confirmed by every operator correlation, and three independent tests agree - our own L test on the P2(1)2(1)2(1) merge it was demoted into, xtriage on that same merge ("no twinning is suspected... most likely due to an NCS axis parallel to the twin axis"), and the arithmetic that a twin at the implied fraction caps twin-pair correlation at 0.55 while the four added operators score 0.84-0.90. Its excess is the coverage limit the comment above the bound already names: the added 422 operators exchange h and k, so they carry a systematic floor the parent's sign-flipping 2-folds do not. The two populations therefore collide at 1.80 and 1.90, not at 1.70, and the bound now sits at the midpoint of that window. Degrading the data - 4x sigma inflation, or an eighth of the sweep - drives the ratio towards 1 and never up, and the estimator is precise (bootstrap standard error 0.2-3.7% of the ratio), so the collision is a genuine population overlap rather than sampling noise. That also rules out scaling the bound by its own error, which at any useful multiple refuses half the battery. Inert on the shipped defaults: no crystal in the battery reads between 1.70 and 1.85 there. It changes one assignment on an experimental integration radius, from wrong to right. The committed twin test is unaffected - genuine promotions in that harness read 0.959-1.016 against 4.23-5.36 for its twin, so nothing lies in the interval that moved. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 19:17:16 +02:00
leonarski_fandClaude Opus 5	80e10f51b3	rugnux: measure and report diffraction anisotropy ... rugnux now says whether a dataset's fall-off is direction-dependent, and by how much. It corrects nothing and truncates nothing: no intensity is changed, no reflection is dropped on a directional criterion, and the written files do not depend on direction at all. Two quantities, because they are not the same thing. The anisotropic deltaB is the range of the principal components of the anisotropy tensor - a rate of fall-off. The diffraction limit along each principal direction is where <I/sigma(I)> in a 20 degree cone falls through 2 - where signal actually runs out. One battery case has only 0.28 A between its directional limits and a 58x ratio in cone <I/sigma>, so reporting either alone would miss it. The tensor is a Laue-constrained deviatoric ADP tensor fitted on INTENSITIES with no positivity cut, by weighted Gauss-Newton over 12 shells x 60 directions with a free constant per shell. Fitting amplitudes after a positivity cut, which is what xtriage and ctruncate do, destroys about 40% of the measured anisotropy - the cut keeps only the positive noise excursions in whichever direction has died, and that is the direction carrying the signal. Against the same 38 merged files rugnux reads 1.24x xtriage's eigenvalue spread and 1.61x ctruncate's; on strong near-isotropic data all three agree to a few percent, and they diverge exactly where a direction has died. The verdict is gated three ways - not detected, detected, or cannot determine - against the dataset's own systematic floor, measured in the tensor directions its Laue symmetry forbids. The floor cannot be measured on merged reflections, which have exact Laue symmetry by construction, so the floor is taken from the unmerged observations and the verdict is "cannot determine" without them. Triclinic has no forbidden subspace and always returns cannot determine. A cubic crystal returns exactly zero, because that is its symmetry and not a measurement. A second axis reports the resolution signature: a genuine Debye-Waller fall-off is linear through the origin in s^2, and a deficit that is flat is something else. Magnitude alone had promoted a crystal that is 68% not a Debye-Waller B into the top five of this battery; it now reads not detected with the caution attached. Following Sheriff & Hendrickson (1987) Acta Cryst. A43, 118-121 for the tensor and Popov & Bourenkov (2003) Acta Cryst. D59, 1145-1153 for the estimator. The directional limits are written as jfjoch_ local mmCIF items rather than _reflns.pdbx_aniso_diffraction_limit_*, whose dictionary definition is explicitly the ellipsoid fitted to a diffraction cut-off surface - a construction rugnux does not perform. The generic anisotropic B tensor items are written. Changes no existing number; only REPORT_VERSION moves, 1 to 2. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 19:13:16 +02:00
leonarski_fandClaude Opus 5	0f5a6e41d6	rugnux: report the Wilson B in --mode scale, and correct what the docs claim about the fixed integration radius ... --mode scale called AnalyzeTwinning but not CalcGlobalWilsonB, so WILSON_B= read nan there. Mirrors what --mode mx does; on one crystal scale mode now reports 72.03 against mx mode's 71.91 on the same data, and where the fitted B is not positive it still reads nan, which is the same verdict --mode mx reaches. The merged .mtz and .hkl are byte-identical before and after. docs/CPU_DATA_ANALYSIS.md and BraggStencil.h both said the flux the fixed r1 disk does not capture "is a function of resolution alone, which the per-shell scale absorbs". Neither half is true. The loss carries a directional component of several A^2 on top of the isotropic part. There is no per-shell scale, and there cannot usefully be one: every scale is fitted against a reference built from a reflection's own symmetry equivalents, equivalents share s^2 exactly, so any function of s^2 lies in the exact null space of the scaling model. What actually absorbs the isotropic part is the Wilson B, which is degenerate with it - so WILSON_B and _reflns.B_iso_Wilson_estimate carry an r1-dependent bias, measured at 18 A^2 of spread across four radius triplets on one crystal. The text also corrected a third error: in the default gaussian mode r1 is not the integration domain at all - the intensity is a profile-fit amplitude over a grid set by r2 - and a note now sits at the section a reader looking up the Wilson B actually lands on. Comments and documentation only for that part; verified by rebuilding and confirming byte-identical output with no flags. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 18:51:06 +02:00
leonarski_fandClaude Opus 5	8db8267ff8	PCIe driver: build DKMS modules for the target kernel, not the running one ... dkms.conf quoted the make binary: MAKE="'make' -C src/ all". dkms passes the kernel it is building for by rewriting the leading "make" of that string into "make -jN KERNELRELEASE=$kernelver" (dkms 3.2.1, line 1446) - an anchored prefix substitution that the quotes defeat, so nothing was ever injected. The Makefile then hardcoded /lib/modules/$(shell uname -r)/build and would have ignored it in any case. With AUTOINSTALL=yes the module was therefore always compiled against the running kernel and installed into the tree of whichever kernel dkms was building for. A dnf update that pulls in a new kernel builds against the old one and drops the result in the new kernel's /extra, where it fails to load on the next boot. Crossing RHEL 9.4 to 9.5 it would also compile the wrong side of the vm_flags guard, which is how this was noticed. The Makefile now takes KDIR, defaulting to the running kernel exactly as before, and dkms.conf passes ${kernel_source_dir} - which dkms resolves for the target kernel before sourcing the conf, and which honours --kernelsourcedir. Dropping the quotes also lets dkms's -jN through, so the recursive invocations become $(MAKE) to keep the jobserver. Verified by building against a kernel other than the running one: the module now comes out carrying the target kernel's vermagic. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PLMZgfMEdtPBZt1F2rNbRA	2026-08-25 17:40:52 +02:00
leonarski_fandClaude Opus 5	59ebe8d9ae	PCIe driver: guard vm_flags_set for RHEL, which backported it into 5.14 ... RHEL and its derivatives report LINUX_VERSION_CODE 5.14.0 for the whole of el9 while backporting newer kernel APIs into it, so the version check alone picked the pre-6.3 branch on every el9 >= 9.5 and the module failed to build with "assignment of read-only member 'vm_flags'". HAVE_VM_FLAGS_SET could override it, but nothing sets it and dkms.conf does not pass it, so a build from the RPM had no way to reach it. vm_flags_set() and the const vm_flags member appear between kernel-5.14.0-440 and -450.el9, during the 9.5 development stream. RHEL_MINOR tracks the released minor exactly, so RHEL_RELEASE_CODE >= RHEL_RELEASE_VERSION(9,5) is the test: 9.0-9.4 (GA -427) do not have them, 9.5 (-503), 9.6 (-570), 9.7 (-611) and 9.8 (-655) do. el10 is 6.12-based and LINUX_VERSION_CODE already covers it, as it does the removal of no_llseek that the other guard in this driver handles. Spelled through a JFJOCH_RHEL_GE() helper rather than inline, because the obvious form #if defined(RHEL_RELEASE_CODE) && RHEL_RELEASE_CODE >= RHEL_RELEASE_VERSION(9,5) is a hard error on both gcc and clang for every non-RHEL kernel: && does not short-circuit past a parse error, and the undefined function-like macro leaves "0 (9,5)" behind. Also corrects > to >= on the upstream check. The wrappers landed in 6.3, so a vanilla 6.3.0 kernel was taking the pre-6.3 branch. Generated code on el8 is unchanged. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PLMZgfMEdtPBZt1F2rNbRA	2026-08-25 17:40:44 +02:00
leonarski_fandClaude Opus 5	ef07770c5f	rugnux: name the unmerged export from the prefix, and drop centring absences ... --export-unmerged and --export-unmerged-partials no longer take a filename; they write <prefix>_unmerged.mtz and <prefix>_unmerged_partials.mtz, as --write-process-h5 already does for <prefix>_process.h5. Lattice-centring absences are no longer written. They are integrated on purpose - prediction runs in P so the space-group search can confirm or disprove the centring - but in an exported file they cost the reader the answer: pointless reads the interstitial nodes, takes the lattice for primitive, and demotes I23 to P2_1 3, while aimless roughly halves its <I/sigma> merging them. They were also only present when the indexer had settled on the conventional centred cell, so the file's content depended on which of two equivalent cells it picked. Screw and glide absences are still written. They are the evidence a space group is chosen on, so a program reading this file can check that choice independently; deleting them turns pointless's test into an assumption ("we cannot determine if the reflections are truly systematically absent"). Deleting them changes no merging statistic. XDS and DIALS draw the line in the same place - XDS ships screw absences and never measures a centring one, and DIALS's absence machinery has only screw-axis classes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 17:21:21 +02:00
leonarski_fandClaude Opus 5	bb5aaca68e	rugnux: sum each rotation reflection's partials into one full on export ... --export-unmerged now writes one row per reflection with its partials summed, which is how a rotation dataset is normally handed to a scaling program. The previous behaviour is still available as --export-unmerged-partials. Partials made the file's usefulness depend on the reading program's partial-assembly settings. On an orthorhombic case only 31% of partial sets passed aimless's default PARTIALS test, so it merged 2% of the file: multiplicity 4.7 against our own 12.4, CC1/2 0.788, and CC against our merged intensities 0.806. Summed, aimless uses 89% of the file and rejects nothing: multiplicity 12.5, CC1/2 0.931, completeness 96.1 to 98.0, pointless Laue confidence 0.669 to 0.792, CC 0.848. The other two test crystals are ties overall and win their outer shells, and the anomalous signal comes out stronger from the fulls. iotbx.merging_statistics, which never assembled partials at all, now reports real merging statistics rather than statistics of parts. Events are grouped by Combine()'s own rule so the file and the merge assemble exactly the same reflections; the sum is plain with variances in quadrature and no partiality division, which reproduces the merge's full times FRACTIONCALC to a few percent. Per-part metadata is combined on a partiality-weighted centroid rather than an intensity-weighted one: 8-41% of events have parts summing to zero or less, where intensity weights are undefined or sign-flipped, and 10-21% of intensity-weighted centroids fall outside the event's own frame range. Events below --min-partiality are not written. Declaring a reflection whose rocking curve caught a thousandth of itself as a complete measurement gives a scaling program noise with a small sigma and it weights it heavily; there is no partial test to catch it once it is a full. This is the same constant already applied to the same quantity in the merge, and it is what takes the orthorhombic case from CC 0.219 to 0.848. --min-partiality 0 writes every event. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 16:18:14 +02:00
leonarski_fandClaude Opus 5	86b7e07131	Drop Ceres' LAPACK, METIS and SuiteSparse back-ends: nothing calls them ... Every Ceres solve in the project selects a dense linear solver explicitly -- DENSE_QR in PostRefine, RingOptimizer and StillsPartialityRefine, DENSE_NORMAL_CHOLESKY in XtalOptimizer, DENSE_SCHUR in GeometryRefiner -- and none of the seven Solver::Options sites sets dense_linear_algebra_library_type, which defaults to EIGEN. ceres::Covariance, the other SuiteSparse consumer, is never instantiated. So no sparse factorization and no LAPACK call is reachable. Measured rather than argued: an LD_PRELOAD shim exporting dgeqrf_, dpotrf_, dtrtrs_, spotrf_ and METIS_NodeND, each aborting on entry, let a full mx run (1800 frames, index -> refine -> integrate -> scale -> merge) finish with every counter at zero. The change is a no-op on results. Baseline and modified binaries produce byte-identical run.mtz, run.hkl and run.cif on a rotation dataset at -N 1, and two baseline runs give that same signature, so the comparison is meaningful. Only the DATE= stamp in the report differs. What it buys is six fewer shared libraries: libopenblas and libmetis, plus libgfortran, libquadmath, libgomp and libz behind them. rugnux links its own zlib statically -- zero undefined zlib symbols before and after -- so the dynamic libz only ever arrived through OpenBLAS. It also makes the build reproducible across hosts. SUITESPARSE defaults ON and self-disables only when its probe fails, so a machine where SuiteSparse_DIR is not found already compiled CERES_NO_SUITESPARSE while one carrying the SuiteSparse CMake config would not have. Pinning it removes that divergence, and shortens what a cross-compiled aarch64 build has to supply. EIGENSPARSE stays ON, so a sparse solver remains available if one is ever selected, without an external library. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 15:58:34 +02:00
leonarski_fandClaude Opus 5	5248b1bc00	rugnux: export the integrated observations as an unmerged MTZ ... Adds --export-unmerged <file.mtz>, in --mode mx and --mode scale alike. rugnux could only write merged reflections, which closed it off from the programs that consume unmerged observations - aimless, pointless, careless and iotbx.merging_statistics all read this file. The column layout follows what pointless itself writes (H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP FLAG), with DELPHI, ZETA, BGMEAN and BGVAR added because we have them and a scale model can use them. Three details decide whether the file is usable: Lorentz-polarization is applied and recorded in LP. It is per-observation geometry spanning a factor of ~120 across a sweep and no reading program can recover it; merging with no scale model at all gives R_meas 0.372 / 0.346 / 0.324 in the low shells without it against 0.183 / 0.218 / 0.257 with it. The partiality is not divided out - it stays in FRACTIONCALC - and neither is the per-image scale, since these programs fit their own. The observations are partials and are flagged as such, packed as 256*M + ISYM with LDTYPE=1. Without the flag pointless reads every part as a whole observation and mis-assigns the symmetry; with it, a tetragonal case assembles 8.29M parts into 1.15M observations and comes back as its own space group at confidence 0.92. The scan axis is written as the negation of the stored goniometer axis, which is the Cambridge convention: against pointless's own orientation matrix that agrees to 0.6 degrees, where the axis as stored disagrees by 40. Merging the exported file with aimless reproduces rugnux's own merge to CC 0.9997 on a tetragonal case and 0.9978 on a cubic one, and the anomalous signal survives. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 15:21:57 +02:00
leonarski_f	61c603b274	v1.0.0-rc.163 (#73) ... * Packaging: each package installs its license notices under a directory of its own - `share/doc/jfjoch_broker`, `share/doc/jfjoch_writer`, `share/doc/jfjoch_viewer`, `share/doc/jfjoch_driver_dkms` - instead of all of them into the shared `share/doc/jfjoch`, so `jfjoch` and `jfjoch-writer` can be upgraded one at a time instead of only together. Reviewed-on: #73 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.163	2026-08-25 13:38:29 +02:00
leonarski_fandjungfrau	4dc2534dbf	v1.0.0.rc-162 (#72) ... **Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one. * HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected. * HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it. * HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset. * HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts. * HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout. * A grid scan and a goniometer axis can both be set; they are no longer alternatives. * `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000. * The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned. * The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer. * rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it. * rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`. * rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way. * rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound. * rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached. * rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use. * rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own. * rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement. * rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged. * rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged. * Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged. * A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses. * rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given. * CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer. * The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2. * Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact. **Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`): * `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file. * `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them. --------- Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch> Reviewed-on: #72 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.162	2026-08-25 08:21:39 +02:00
leonarski_f	538f3504d3	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> 1.0.0-rc.161	2026-08-13 17:03:10 +02:00
leonarski_f	67dca388bd	v1.0.0-rc.160 (#70) ... 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: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.160	2026-07-19 09:39:28 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... 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: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.159	2026-07-13 13:54:03 +02:00
leonarski_f	451310f43d	v1.0.0-rc.158 (#68) ... 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. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.158	2026-07-12 19:42:29 +02:00
leonarski_f	54c0100e8e	v1.0.0-rc.157 (#67) ... 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: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.157	2026-07-11 07:19:11 +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> 1.0.0-rc.156	2026-07-03 19:18:56 +02:00
leonarski_f	54c667190f	v1.0.0-rc.155 (#65) ... 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: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65 1.0.0-rc.155	2026-06-25 22:01:48 +02:00
leonarski_f	6136f858af	v1.0.0-rc.154 (#64) ... 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_broker: Fix to TCP file pusher (remove kernel zero copy to improve reliability) Reviewed-on: #64 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.154	2026-06-25 18:12:00 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63 1.0.0-rc.153	2026-06-23 20:29:49 +02:00
leonarski_f	c49bd2ac3b	v1.0.0-rc.152 (#62) ... * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5) * jfjoch_viewer: Adjust Q bounds for azimuthal integration * jfjoch_azint: Add tool to do quick azimuthal integration Reviewed-on: #62 1.0.0-rc.152	2026-06-17 20:36:24 +02:00
leonarski_f	ef52dac2ee	v1.0.0-rc.151 (#61) ... * jfjoch_broker: For PSI EIGER detector allow to disable individual half-modules by putting empty hostname Reviewed-on: #61 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.151	2026-06-16 14:13:29 +02:00
leonarski_f	90e804acd7	v1.0.0-rc.150 (#60) ... * jfjoch_broker: When in FPGA workflow (with PSI detectors) azimuthal integration might be forced to CPU - this will require more computational power, but it enables more integration bins and reports standard deviation of each bin. * jfjoch_broker: Raise error if one is in FPGA flow and there are too many azimuthal integration bins. Reviewed-on: #60 1.0.0-rc.150	2026-06-15 20:24:15 +02:00
leonarski_f	ea575f790a	v1.0.0-rc.149 (#59) ... * XDS plugin: Fix HDF5 mutex to run on multiple processors Reviewed-on: #59 1.0.0-rc.149	2026-06-13 21:27:41 +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 1.0.0-rc.148	2026-06-08 08:30:35 +02:00
leonarski_f	75de40f52b	v1.0.0-rc.147 (#57) ... 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_viewer: Add reciprocal space viewer * jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset * jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress) Reviewed-on: #57 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-02 11:49:24 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... 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_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56 1.0.0-rc.146	2026-05-28 18:48:35 +02:00
leonarski_f	75f1c5f954	SHIM library improvements from the HDF Group	2026-05-08 11:39:51 +02:00
leonarski_f	caef26873e	v1.0.0-rc.145 (#55) ... This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144. * **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future. * XDS plugin: Improve performance of VDS reading. * jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD. * jfjoch_writer: Clean-up of HDF5 routines to better handle issues. Reviewed-on: #55 1.0.0-rc.145	2026-05-06 21:50:02 +02:00
leonarski_f	7d34e8a049	v1.0.0-rc.144 (#54) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve performance of preview JPEG image generator at receiver startup (saving about 150 ms on measurement start for 16M) Reviewed-on: #54 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.144	2026-05-01 17:06:36 +02:00
leonarski_f	6e0bb971ac	v1.0.0-rc.143 (#53) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Avoid copying gain calibration together with DiffractionExperiment Reviewed-on: #53 1.0.0-rc.143	2026-04-30 22:16:50 +02:00
leonarski_f	87fde1b32e	v1.0.0-rc.142 (#52) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Support for newer CUDA architectures (notably Blackwell); minimum CUDA version 12.8 * Minor changes to jfjoch_process, jfjoch_fpga_test and jfjoch_lite_perf_test to make them more consistent Reviewed-on: #52 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 16:47:53 +02:00
leonarski_f	d760b12a18	v1.0.0-rc.141 (#51) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times * frontend: Fix selection of FFTW in indexing settings Reviewed-on: #51 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 13:04:54 +02:00
leonarski_f	239a441ee6	v1.0.0-rc.140 (#50) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection * jfjoch_broker: Minor bug fixes for rare conditions Reviewed-on: #50	2026-04-29 21:40:22 +02:00
leonarski_f	4878318c27	v1.0.0-rc.139 (#49) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start` * jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start' * jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time * jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received * jfjoch_broker: Use nanoseconds internally for frame/image/readout time * jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished) * jfojch_broker: Improve profiling of different data analysis steps * jfjoch_broker: Record integration reflection count * jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds) * jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked * jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets **Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time. Reviewed-on: #49 1.0.0-rc.139	2026-04-29 09:50:50 +02:00
leonarski_fandtakaba_k	230480e390	v1.0.0-rc.138 (#48) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Cleanup DECTRIS start-up code to enable a shorter start time jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations jfjoch_broker: Goniometer axis name is converted to lowercase jfjoch_broker: Fix bug, where wrong HTTP error codes were returned jfjoch_broker: Improve sigma estimation during merging (K. Takaba) --------- Co-authored-by: takaba_k <kiyofumi.takaba@psi.ch> Reviewed-on: #48 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.138	2026-04-27 19:56:14 +02:00
leonarski_f	c981e1b91c	v1.0.0-rc.137 (#46) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Better track time for each operation in the processing stack * jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress) * jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress) * jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0) Reviewed-on: #46 1.0.0-rc.137	2026-04-25 19:59:21 +02:00
leonarski_f	c1c170112c	v1.0.0-rc.136 (#45) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve logic regarding indexing architecture and thread pools (work in progress). Reviewed-on: #45 1.0.0-rc.136	2026-04-20 11:54:33 +02:00
leonarski_f	bb9f5c715f	v1.0.0-rc.135 (#44) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.135	2026-04-16 11:59:59 +02:00
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43 1.0.0-rc.134	2026-04-09 13:30:47 +02:00
leonarski_f	81bd9a06a1	CI pipeline upgrade (#42) ... Updates to CI pipeline * New docker image for Ubuntu 22.04 with CMake 3.26 * New docker image for Rocky 9 with DIALS 3.27 * New automated test to check for DIALS processing with xia2.ssx Reviewed-on: #42	2026-03-28 20:06:23 +01:00
leonarski_f	6133da1377	v1.0.0-rc.133 ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Use httplib for HTTP server instead of Pistache * jfjoch_broker: Drop OpenSSL support * jfjoch_broker: Base work for multi-lattice support in the future * Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib) Reviewed-on: #41 1.0.0-rc.133	2026-03-26 20:50:33 +01:00
leonarski_f	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40 1.0.0-rc.132	2026-03-12 12:17:11 +01:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39 1.0.0-rc.131	2026-03-07 11:34:04 +01:00
leonarski_f	928789a67c	v1.0.0-rc.130 (#37) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Rotation indexer has two retries if failes * jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot) * jfjoch_broker: Integration calculates background mask based on R2 radius * jfjoch_process: HDF5 files are not saved by default Reviewed-on: #37 1.0.0-rc.130	2026-03-06 14:38:56 +01:00
leonarski_f	64002f1e29	v1.0.0-rc.129 (#36) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files) * jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction * jfjoch_broker: Image pusher statistics are accessible via the REST interface * jfjoch_writer: Supports TCP image socket and for these auto-forking option Reviewed-on: #36 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.129	2026-03-05 22:13:12 +01:00