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Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	800ffecd20	process/viewer: command-line generator + JFJochProcessController (GUI engine) ... Foundation for making processing a first-class GUI activity: - process/JFJochProcessCommandLine: reconstruct the equivalent jfjoch_process / jfjoch_azint command line from a ProcessConfig + DiffractionExperiment + input path, for handing a job off to a cluster. Unit-tested (full + azint). - viewer/JFJochProcessController: runs one JFJochProcess job off the GUI thread (its own private reader; HDF5 access is globally serialized so it is safe next to the interactive reader) and reports back via queued Qt signals (started/phaseChanged/progress/finished/failed). Cancel() forwards to JFJochProcess::Cancel(). Progress is throttled to ~200 updates per run. The visible processing UI (jobs window + snapshot switcher + converged settings) builds on this. Verified: tests/jfjoch_test [process]; jfjoch_viewer links and builds against JFJochProcess. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 14:26:48 +02:00
leonarski_fandClaude Opus 4.8	39599bc090	tests: git-LFS large-dataset harness + jfjoch_process include cleanup ... - .gitattributes tracks tests/data/*.h5 via git-LFS for big reference datasets. - tests/TestData.h resolves tests/data files and reports absent / unfetched-LFS-pointer so tests can SKIP() instead of failing; tests/data/README.md documents fetching + the expected lyso_rotation/lyso_serial datasets. - JFJochProcessLargeTest: a Catch start-up listener that prints dataset availability, plus [large] full-analysis runs (rotation indexing + serial) that SKIP when data is absent. Verified against the real 1800-image lyso rotation set (100% indexing, cell 78.2/78.2/37.8) and skips cleanly without it. - jfjoch_process.cpp: drop the ~15 now-unused workflow includes left after the JFJochProcess extraction. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 14:16:34 +02:00
leonarski_fandClaude Opus 4.8	4697f10555	process: extract reprocessing workflow into shared JFJochProcess library ... The full processing workflow no longer lives in the CLIs. New process/JFJochProcess encapsulates it for jfjoch_process, jfjoch_azint and (later) the viewer: - ProcessMode {AzimuthalIntegration, FullAnalysis}; ProcessConfig carries run control (range, threads, output prefix, spot finding, rotation + scaling options, reference data) while the DiffractionExperiment carries all algorithm settings. - Run() executes setup -> optional two-pass rotation pre-pass -> parallel per-image loop (std::thread) -> optional scaling/merging post-pass -> NXmxIntegrated _process.h5 that links back to the original images. ProcessResult returns stats + merge text. - Cancel() / std::atomic<bool> (receiver style), checked between images; the CLIs install a SIGINT handler that calls it (fixes the previous Ctrl+C gap), the viewer will use the same hook. JFJochProcessObserver streams progress / per-image results for a live GUI. jfjoch_process.cpp and jfjoch_azint.cpp are now thin: argument parsing + experiment configuration, then JFJochProcess::Run + stats printing. Behaviour and usage messages are unchanged. Adds JFJochProcessTest (azimuthal integration round-trip, no-output run, pre-cancel) over a small generated dataset. Verified: tests/jfjoch_test [HDF5] (83 cases / 1854 assertions); jfjoch_azint and jfjoch_process run end-to-end on lyso_test (azint 20 images; full analysis recovers the lysozyme cell at 25% indexing). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 10:36:18 +02:00
leonarski_fandClaude Opus 4.8	9434878c92	reader: split metadata reading into HDF5MetadataSource + snapshot map ... Complete the image/metadata decoupling. JFJochHDF5Reader is now a thin JFJochReader facade composing one shared HDF5ImageSource (raw pixels) with a name->HDF5MetadataSource map and an active selection ("snapshots"). - HDF5MetadataSource owns one master file: dataset-level parse (Open, ex-ReadFile), per-image metadata (FillPerImage, ex-LoadImage_i), ReadSpots/ReadReflections/ ReadCalibration, and the master-first helpers. It locates per-image metadata either via the shared image source (original file: metadata co-located with pixels) or in its own master at the global index (integrated _process.h5 snapshot) - so switching snapshots never reloads pixels. - Facade adds RegisterSnapshot/SetActiveSnapshot/SnapshotNames/ActiveSnapshot; ReadFile registers the original as "Original". All existing JFJochReader callers are unchanged. - The global hdf5_mutex is taken once in the facade; the sources assume it is held. Adds JFJochReader_Snapshots test (original _master.h5 + a reprocessing _process.h5 over the same images: pixels stay from the original, metadata follows the active snapshot). Verified: tests/jfjoch_test [HDF5] (80 cases / 1810 assertions), plus jfjoch_process/ azint/extract_hkl/scale and jfjoch_viewer all build against the refactored reader. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 10:15:09 +02:00
leonarski_fandClaude Opus 4.8	23d27f30c4	reader: split raw-image reading into HDF5ImageLocator + HDF5ImageSource ... Decouple the raw-pixel side of JFJochHDF5Reader from the rest as the first step toward swappable per-dataset metadata snapshots. - HDF5ImageLocator: single owner of the legacy/VDS/contiguous layout resolution plus a persistent open-file cache, replacing the four duplicated resolvers (GetImageLocation, ReadSpots, ReadReflections) and their per-call file caches. Also hosts the source-mapping logic (former GetHDF5DataSource body). - HDF5ImageSource: raw-pixel reading (locator + LoadImageDataset); the part whose links to files stay fixed while the metadata master may change. - JFJochHDF5Reader keeps a thin GetImageLocation/GetRawImage/GetHDF5DataSource that delegate to image_source_; the six layout members are gone, parsed into a local Layout handed to the source at the end of ReadFile. Cache cleared on Close(). Verified: tests/jfjoch_test [HDF5] (79 cases / 1775 assertions), and jfjoch_process/azint/extract_hkl/scale relink unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 10:15:09 +02:00
leonarski_fandClaude Opus 4.8	ec8a45dc09	windows: bundle cuFFT in installer and tag the CUDA/CPU variant ... cuFFT is the only CUDA component linked dynamically (cudart and the fast-feedback indexer are static), so the prior Windows installer would fail to launch the GPU path on a host without a CUDA toolkit. Ship cufft64_*.dll next to the viewer (CUDA 13 keeps it in bin/x64, earlier toolkits in bin); the DLL is self-contained, so the installed app needs only an NVIDIA driver. Tag the variant where it matters and nowhere else: the installer filename (-cuda<major> / -cpu) and the Add/Remove Programs entry ("Jungfraujoch (CUDA)" / "(CPU)") advertise it, while the install folder and Start Menu group stay plain "Jungfraujoch" -- the CUDA build is a strict superset, so the two variants share a location and replace each other. Docs: SOFTWARE.md + JFJOCH_VIEWER.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-21 09:17:52 +02:00
leonarski_fandClaude Opus 4.8	0c1babd0ca	CMake: provide Eigen externally again; fix cpack NSIS icon escape ... Revert Eigen from the FetchContent OVERRIDE_FIND_PACKAGE vendoring (cd394c52, d4d2d0d8) back to an external find_package(Eigen3) dependency, like zlib. The OVERRIDE_FIND_PACKAGE mechanism makes the Visual-Studio-bundled CMake (4.x "-msvc") intermittently segfault during configure -- ~1/3 of fresh configures, and 100% with Ceres CUDA enabled. The fault is in CMake's own FetchContent variable-stack cleanup, reached when Ceres' find_package(Eigen3) resolves the override through a nested FetchContent_MakeAvailable. Stock Kitware CMake runs the identical scripts fine, so it is a bug in the VS-bundled cmake binary; providing Eigen externally avoids that path entirely and is stable with Ceres CUDA both on and off (verified 0 crashes; full CUDA build + NSIS installer succeed under the VS-bundled cmake). Also fix CPACK_NSIS_INSTALLED_ICON_NAME: the backslash value was written verbatim into CPackConfig.cmake, where "\j" is an invalid escape that cmake 4.x (CMP0010 strict) rejects when cpack re-parses it, so cpack failed under the VS-bundled cmake (older/Kitware cpack only warned). Use a forward slash. - image_analysis: keep Ceres USE_CUDA OFF (Jungfraujoch does not use Ceres' GPU solvers) but drop the now-obsolete "required to avoid the Windows cmake crash" rationale from the comment. - docs: Eigen is a required external dependency again (SOFTWARE.md); the Windows viewer build provides zlib + Eigen externally (JFJOCH_VIEWER.md). - THIRD_PARTY_NOTICES: move Eigen from the fetched-and-linked table to the external runtime-libraries table. Docker images still need Eigen re-added (5.0.1, source build) -- to follow. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-20 22:33:12 +02:00
leonarski_fandClaude Opus 4.8	1ea5897fca	windows: vendor wingetopt and scope server-only targets out of viewer-only builds ... MSVC/Windows build fixes: - Force JFJOCH_VIEWER_ONLY ON for Windows and macOS; the broker/receiver/FPGA/ writer server stack is Linux-only, so those platforms build the viewer subset. - Vendor an OpenBSD/NetBSD getopt/getopt_long shim (tools/wingetopt/, BSD/ISC) as a WIN32-only static lib -- the MSVC CRT has no <getopt.h> -- and link it into the four portable CLI tools on Windows. - jfjoch_extract_hkl.cpp: include <getopt.h> explicitly (it relied on glibc's transitive <unistd.h>). - jfjoch_process.cpp: guard <unistd.h> with #ifndef _WIN32. - Guard JFJochStreamWriter and jfjoch_writer with IF(NOT JFJOCH_VIEWER_ONLY): the former pulls in JFJochImagePuller, the latter uses a fork()/waitpid() multi-process design; neither belongs to the portable viewer subset. - Record wingetopt in THIRD_PARTY_NOTICES.md and licenses/. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 18:50:20 +02:00
leonarski_fandClaude Opus 4.8	e5034d0a2c	licenses: add third-party notices, attribution texts, and viewer license window ... Acknowledge all bundled third-party software and satisfy attribution/notice requirements, while keeping it maintainable: - THIRD_PARTY_NOTICES.md: human-readable manifest (component, copyright, SPDX license, link) for fetched, vendored, and runtime/SDK dependencies. - licenses/: verbatim license texts; COLLECT.sh regenerates them from the build trees and system SDK locations. - Bundle the verbatim Qt LGPL-3.0 text and the CUDA Toolkit 12.8 EULA. - frontend: self-contained npm attribution generator (`npm run licenses` -> dist/THIRD_PARTY_LICENSES.txt), wired into the frontend build target. - Install LICENSE + notices + licenses/ into share/doc/jfjoch for every packaged component. - viewer: Help > "Third-party Licenses" window (QTextBrowser) showing a generated, self-contained HTML built from licenses/. - docs/SOFTWARE.md: drop the stale hand-kept dependency lists; point at the manifest. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 18:35:50 +02:00
leonarski_fandClaude Opus 4.8	e035f7c303	viewer: drop unused CMAKE_AUTORCC ... The viewer's only .qrc is compiled explicitly via QT_ADD_RESOURCES into APP_RESOURCES; no .qrc is added directly as a target source, so AUTORCC never acted on anything. Remove the dead flag. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 17:22:48 +02:00
leonarski_fandClaude Opus 4.8	f9396e01e7	viewer: Windows NSIS / macOS installer polish + bundle analysis CLIs ... NSIS installer was missing several things on Windows: - License: show the repo GPLv3 LICENSE as the click-through license page (CPACK_RESOURCE_FILE_LICENSE). - Start Menu: no shortcut was created -- add CPACK_PACKAGE_EXECUTABLES for jfjoch_viewer, and embed an app icon so the shortcut is not generic. The icon is a new multi-size jfjoch.ico (256 PNG + 48/32/16) compiled into the .exe via resources/jfjoch.rc; macOS gets the matching jfjoch.icns copied into the .app bundle (MACOSX_BUNDLE_ICON_FILE). Both derived from resources/jfjoch.png, padded square with transparent bands. - Naming: install folder, Start Menu group and Add/Remove Programs entry are now "Jungfraujoch" instead of "jfjoch <version>". Also ship the offline analysis CLIs (jfjoch_process/scale/azint/extract_hkl) in viewer-only / Windows packages: JFJochReceiverPlots now lives in JFJochCommon, so their stale JFJochReceiver link is dropped, leaving only the portable libs (reader/image_analysis/writer/common). tools/CMakeLists.txt is split so those four build everywhere while the hardware tools stay gated behind NOT JFJOCH_VIEWER_ONLY, and the viewer-only branch now adds tools/. They install into the "viewer" CPack component. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 16:40:46 +02:00
leonarski_f	e6c6536e3a	JFJochReceiverPlots: Move to common/, so it can be linked without bringing JFJochReceiver HW dependencies	2026-06-20 16:26:11 +02:00
leonarski_fandClaude Opus 4.8	5247acc07e	CMake: package the viewer component in JFJOCH_VIEWER_ONLY builds ... A viewer-only build builds jfjoch_viewer but the CPack block hard-coded CPACK_COMPONENTS_ALL to "jfjoch writer" and only appended "viewer" when JFJOCH_VIEWER_BUILD was set -- which a pure viewer-only build does not set. cpack then tried to package the empty jfjoch/writer components and failed, requiring a manual -D CPACK_COMPONENTS_ALL=viewer. Branch the component list on build mode: viewer-only packages just "viewer"; other modes keep "jfjoch writer" plus driver-dkms/viewer when their flags are set. Also drops the redundant re-set of the default list. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 16:13:24 +02:00
leonarski_fandClaude Opus 4.8	5064b5ba47	image_analysis: force Ceres to build without CUDA ... USE_CUDA is a Ceres cache STRING (default "default" = auto-detect), not an option(), so a plain SET was shadowed by the cache default and CUDA got enabled on MSVC. Force it OFF in the cache instead. Also drop two dead settings: MINIGLOG (Ceres uses abseil logging now, no longer referenced) and EIGENSPARSE ON (already Ceres' default). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 16:08:38 +02:00
leonarski_f	a89a4c5beb	jfjoch_viewer: Show detected GPUs in the about box	2026-06-20 16:08:13 +02:00
leonarski_fandClaude Opus 4.8	9c9f818ea6	CMake: support DGX Spark (Blackwell GB10 sm_121 + aarch64 FFTW NEON) ... - CUDA: append sm_121 (Blackwell GB10 / DGX Spark) to CMAKE_CUDA_ARCHITECTURES when nvcc >= 12.9 knows it. The static list tops out at sm_120 and embeds no PTX, so without this a build would fail to launch on Spark ("no kernel image available"); guarded so CUDA 12.8 (which predates sm_121) is unaffected. - FFTW: enable NEON codelets on aarch64 (Grace), mirroring the x86 SSE2/AVX/AVX2 branch, so single-precision FFT is SIMD-accelerated instead of scalar on ARM. Both are inert on x86 / CUDA 12.8; verified configure still succeeds there. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 15:42:00 +02:00
leonarski_fandClaude Opus 4.8	8cd46751f9	docker: drop fftw too -- the project builds FFTW itself ... FFTW is fetched and built by the jungfraujoch CMake (single-precision, from the release tarball), so the system fftw packages (fftw-static/fftw-devel on Rocky, libfftw3-dev on Ubuntu) were unused. Remove them from all four images. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 15:32:05 +02:00
leonarski_fandClaude Opus 4.8	da5fff71a9	docker: unify static Qt 6.9.1 on all 4 Linux images, drop dead prebuilds ... The jungfraujoch CMake now builds HDF5 + libtiff (FetchContent) and libjpeg-turbo + Eigen (ExternalProject / OVERRIDE_FIND_PACKAGE) itself, so the per-image pre-builds and system -dev packages for those were dead weight (the app rebuilt its own copies regardless). Consolidate dependency management into the one CMakeLists at the cost of longer build time (build env has network). - Qt: pin static 6.9.1 everywhere. ubuntu2204 was on 6.10.0 and ubuntu2404 used the OS Qt (~6.4, dynamic) -- the latter is now a static 6.9.1 build like the others, so every image ships a self-contained, identical-Qt viewer. - Remove the HDF5/libtiff/libjpeg-turbo/Eigen source builds + their system -dev packages + the stale /opt/* CMAKE_PREFIX_PATH/PKG_CONFIG_PATH entries. - nasm: now needed by the project's libjpeg-turbo ExternalProject; added to ubuntu2404 (the others already had it). - Standardize the Qt configure flags across all four (xcb, xcb_xlib=OFF, no Wayland -- the qtwayland module was never built, so wayland_client=ON on ubuntu2204 was a no-op). Untested here (no Docker on this host) -- needs a build in each image; the ubuntu2404 static-Qt dep list in particular should be sanity-checked. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 15:28:29 +02:00
leonarski_fandClaude Opus 4.8	31630c20a1	viewer: macOS .app / Windows GUI packaging + Qt deploy + CPack generators ... Add the platform packaging the viewer was missing so it can ship as a .dmg (macOS) or installer (Windows): - viewer: set MACOSX_BUNDLE (a .app bundle on macOS) and WIN32_EXECUTABLE (GUI subsystem, no console window) -- both ignored where they don't apply; install with BUNDLE/RUNTIME destinations. - viewer: qt_generate_deploy_app_script + install(SCRIPT) to bundle the Qt runtime at install time (windeployqt on Windows, macdeployqt on macOS). Gated on Qt >= 6.5, which is where the OUTPUT_SCRIPT signature and the Linux deploy path landed; with a static Qt (our Linux builds) it is a no-op. - CPack: select DragNDrop (.dmg) on macOS and NSIS on Windows, ahead of the Linux-only /etc/* probes; DEB/RPM path unchanged. Verified: configures + generates cleanly on Linux with the viewer enabled (Qt 6.4.2 -> deploy step correctly skipped). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 15:05:40 +02:00
leonarski_fandClaude Opus 4.8	d4d2d0d8ad	CMake: fix CI -- export vendored Eigen so Ceres' install(EXPORT) resolves ... A clean configure failed at generation: install(EXPORT "CeresExport" ...) includes target "ceres" which requires target "eigen" that is not in any export set. Ceres' install(EXPORT CeresExport) is unconditional, and its ceres target transitively links the eigen target. As a FetchContent subproject Eigen leaves EIGEN_BUILD_CMAKE_PACKAGE OFF (it defaults to PROJECT_IS_TOP_LEVEL), so its install(EXPORT Eigen3Targets) never runs and eigen ends up in no installed export set. Force EIGEN_BUILD_CMAKE_PACKAGE ON so eigen is exported and Ceres' export validates. Install/export-only change; the build is unaffected. Verified with a clean configure (fresh CMakeCache): configure + generate now succeed where they previously errored. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 13:38:46 +02:00
leonarski_fandClaude Opus 4.8	cd394c5249	CMake: vendor Eigen (5.0.1) and libjpeg-turbo so the build is self-contained ... Two deps the Linux build picked up from the system were absent on Windows. Bundle both, unconditionally (matching how libtiff/FFTW are vendored), so the tree builds without system Eigen/JPEG: - Eigen 5.0.1 via FetchContent with OVERRIDE_FIND_PACKAGE, so every find_package(Eigen3) -- ours, Ceres', and ffbidx' -- resolves to this copy and the requested 3.4 version is satisfied by the newer major. ffbidx's bundled eigen submodule is disabled (GIT_SUBMODULES "" on fast-indexer) so it no longer creates a duplicate Eigen3::Eigen target. Verified on a CUDA build: Ceres 2.3.0, the analysis libs, and ffbidx's CUDA code all compile against 5.0.1. - libjpeg-turbo 3.0.4 via ExternalProject (upstream discourages add_subdirectory); built+installed static and imported as JPEG::JPEG, replacing find_package(JPEG) in preview/. SIMD is lazy: WITH_SIMD=ON + REQUIRE_SIMD=OFF means NASM-accelerated when nasm is present, otherwise a warning and a scalar build (no hard failure). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 07:55:56 +02:00
leonarski_f	4737eff1a9	jfjoch_process: Missing include <set>	2026-06-20 07:44:50 +02:00
leonarski_f	7eb927e82f	CMake: Ensure static ZLIB (must be before FIND_PACKAGE)	2026-06-20 07:40:56 +02:00
leonarski_fandClaude Opus 4.8	1ae2e6869d	CLAUDE.md: record Windows viewer goal of MSVC + CUDA, and unbundled deps ... The recurring goal is a Windows jfjoch_viewer built with MSVC *and* CUDA ON (GPU processing is wanted, not a CPU-only fallback); the non-CUDA path is the macOS fallback. Also note the three deps a self-contained Windows build still needs but FetchContent does not auto-provide: ZLIB (bundle zlib-ng as ZLIB::ZLIB), libjpeg-turbo (ExternalProject), and Eigen (header-only, also needed by Ceres) -- each guarded so the Linux build is unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 07:38:06 +02:00
leonarski_fandClaude Opus 4.8	025c6394b6	reader: fix Windows path handling in JFJochHDF5Reader ... Two spots used POSIX-only path logic that breaks on Windows: - dataset_name() located the basename with rfind('/'), which misses backslash separators, so a C:\...\foo_master.h5 file prefix kept the whole directory. Use std::filesystem::path::filename() instead. - Legacy-format data-file resolution joined paths with fmt::format("{}/{}", ...), producing mixed \/ separators and prepending the master directory even to absolute link targets. Reuse the existing ResolveRelativeToMaster() helper, which joins via std::filesystem and leaves absolute targets untouched. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 07:23:07 +02:00
leonarski_fandClaude Opus 4.8	4a39f2cfcf	Fix FFTW build-tree header wiring and two MSVC warnings ... FFTW exposes fftw3.h only via $<INSTALL_INTERFACE:include>, so consuming fftw3f from the build tree (FetchContent) leaves FFTIndexerCPU.h unable to find the header. A system-installed fftw3.h masks this on Linux, so it only bit on Windows; add the source-tree api/ dir to fftw3f's interface includes. Also two viewer-reachable warnings: - time_utc.h (C4477): %03ld was fed a chrono milliseconds::rep (64-bit), not a long; cast the 0-999 value to int and use %03d. - HDF5Objects.h (C4700): value-initialize the scalar read buffer. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 07:15:47 +02:00
leonarski_fandClaude Opus 4.8	b888c53509	CMake: stop libtiff/httplib pulling in webp, sharpyuv, brotli ... libtiff's webp and lerc codec options default ON whenever their library is found on the build host, dragging in libwebp + libsharpyuv (webp) and libLerc. We only need DEFLATE (zlib) + the internal LZW codec, so turn both OFF. httplib likewise auto-enables Brotli content-encoding when system Brotli is present; gzip/zlib is enough for the broker, so disable it. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-20 07:10:04 +02:00
leonarski_f	a872b68d6f	ADUHistogram: Fix missing exception header	2026-06-20 06:14:15 +02:00
leonarski_fandClaude Opus 4.8	bcd588b400	CMake: build StreamWriter only into JFJochStreamWriter ... StreamWriter.cpp was compiled into both JFJochWriter and JFJochStreamWriter, so JFJochWriter still transitively pulled in image_puller headers via StreamWriter.h. Compile it only into JFJochStreamWriter (which already links JFJochImagePuller); targets needing the streaming writer (jfjoch_writer, jfjoch_test) link that lib, while JFJochWriter consumers (viewer, tools, ImagePusher) no longer drag in the puller. Also drop a stray duplicate HDF5DataFile source listing. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 23:15:49 +02:00
leonarski_fandClaude Opus 4.8	ebc28744e2	viewer: fix MSVC compatibility in viewer-reachable code ... Address portability issues found building jfjoch_viewer with MSVC: - common/{ADUHistogram,AzimuthalIntegrationProfile}.h and image_analysis/spot_finding/StrongPixelSet.h only need DeviceOutput, so include fpga/pcie_driver/jfjoch_fpga.h (plain-C, self-contained) directly instead of acquisition_device/AcquisitionDevice.h, which dragged <unistd.h> into the viewer tree. - common/time_utc.h: guard gmtime_r/timegm/localtime_r with the MSVC equivalents (gmtime_s/_mkgmtime/localtime_s) under _WIN32; drop the duplicated includes and add the headers used directly. - gemmi_gph/gemmi/utf.hpp: vendor the upstream gemmi header; fileutil.hpp includes it on Windows for UTF8_to_wchar but it was never vendored. - writer/HDF5Objects.cpp: ExtractFilename returns path.filename().string() (std::filesystem::path has no implicit conversion to std::string on Windows, where it is wchar_t-based). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 23:15:27 +02:00
leonarski_f	07ce8b785a	CMake: Remove image_puller dependency from the jfjoch_viewer	2026-06-19 23:03:07 +02:00
leonarski_f	c9803ccbfd	Separate JFJochWriter and JFJochStreamWriter	2026-06-19 22:56:11 +02:00
leonarski_fandClaude Opus 4.8	5a6485da3a	cmake: use upstream libtiff (gitlab) at v4.7.1 ... Switch the libtiff FetchContent from the personal GitHub mirror to the upstream gitlab repo and bump v4.6.0 -> v4.7.1 -- cleaner provenance; the mirror was only ever a network-reachability workaround. Verified on Linux: fetches, builds static (libtiff.a/libtiffxx.a), and jfjoch_viewer links cleanly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 22:47:36 +02:00
leonarski_fandClaude Opus 4.8	53645434be	cmake: enable FFTW SSE2/AVX/AVX2 codelets (x86, runtime-dispatched) ... FFTW selects SIMD codelets at runtime via cpuid, so enabling AVX2 does not require an AVX2 CPU -- it just speeds up the CPU FFT fallback indexer on capable hardware and falls back to SSE2/scalar otherwise. Arch-guarded to x86_64/AMD64 (ARM would need ENABLE_NEON). AVX-512 left off on purpose: it's x86-64-v4 (not our v3 target), the FFT gain over AVX2 is marginal, older Intel downclocks on it, and it's the riskiest to build under MSVC. Verified on Linux: SSE2/AVX/AVX2 codelets compile, libfftw3f.a stays a single static archive, jfjoch_viewer relinks cleanly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 22:37:09 +02:00
leonarski_fandClaude Opus 4.8	0220c6376d	cmake: fetch libtiff and FFTW instead of relying on system libs ... Both are leaf deps (JFJochPreview / JFJochIndexing) that only our own code looks for, so building them ourselves removes the system-package lottery and gives a reproducible, statically-linked build on every platform. - libtiff: FetchContent, library only (jbig/zstd/lzma/jpeg/old-jpeg/tools/ tests off). The C++ binding (TIFF::CXX / libtiffxx) is packaged inconsistently across distros -- missing on Rocky 9 -- and absent on Windows, so find_package(TIFF COMPONENTS CXX) was unreliable; that call is removed and JFJochPreview links the tiff/tiffxx targets directly. GitHub mirror because upstream (gitlab) is unreachable from some restricted hosts. - FFTW: FetchContent single precision (ENABLE_FLOAT) from the release tarball -- the git repo ships no pre-generated codelets (needs OCaml genfft). It's now always available, so the CPU FFT indexer is always built and JFJOCH_USE_FFTW always defined; the "FFTW disabled" path is gone. Static (libfftw3f.a) via the global BUILD_SHARED_LIBS OFF. Verified on Linux: jfjoch_viewer builds and links libfftw3f.a + libtiff*.a, all static. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 22:16:05 +02:00
leonarski_f	fcbe19103d	Update to most recent bitshuffle version	2026-06-19 22:10:06 +02:00
leonarski_fandClaude Opus 4.8	0585fab9bf	cmake: don't fetch sls/catch2 in a viewer-only build ... Under JFJOCH_VIEWER_ONLY, only the viewer's transitive deps are built, so sls_detector_package (detector_control/receiver) and catch2 (tests) are never used -- and sls does not configure under MSVC, which is the whole point of the viewer-only mode. Skip fetching just those two; zstd, hdf5, spdlog, libzmq and httplib are still required (JFJochReader links httplib). Verified: cmake -DJFJOCH_VIEWER_ONLY=ON configures with sls/catch2 absent and `make jfjoch_viewer` still links. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 21:02:28 +02:00
leonarski_fandClaude Opus 4.8	3c6439530d	cmake: raise policy floor to 3.5 for FetchContent deps (CMake 4.x) ... CMake >= 4.0 (4.3.1 ships bundled with Visual Studio 2026) makes any cmake_minimum_required(VERSION < 3.5) a fatal error. The fetched libzmq still declares VERSION 3.0.2, which aborts configuration before our own CMakeLists gets a say. Set CMAKE_POLICY_VERSION_MINIMUM=3.5 before the FetchContent_MakeAvailable calls so those subprojects configure; the variable is simply unused (harmless) on CMake < 3.30. Verified against CMake 4.3.1: the real libzmq source fails without it and configures with it, and an in-file SET() propagates into the add_subdirectory child exactly as a -D cache entry does. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 21:02:28 +02:00
leonarski_fandClaude Opus 4.8	f21c22d453	cmake: add JFJOCH_VIEWER_ONLY to build the viewer standalone ... New option (default OFF) that compiles only jfjoch_viewer and the libraries it transitively links -- common, image_analysis, writer, reader, preview, image_puller, frame_serialize, gemmi_gph, compression, jungfrau, and the OpenAPI model (JFJochAPI) -- skipping the Linux-only online stack (broker service, receiver, fpga, acquisition_device, detector_control, image_pusher, xds-plugin, tests, tools) and the frontend. This is the standalone build path for the cross-platform viewer. JFJochAPI is the only piece the viewer needs from broker/, so the broker service library and executable are gated behind NOT JFJOCH_VIEWER_ONLY. The full build and JFJOCH_VIEWER_BUILD (viewer on top of the full build) are unchanged -- that path is the verbatim ELSE() branch. Verified on Linux: cmake -DJFJOCH_VIEWER_ONLY=ON configures and `make jfjoch_viewer` links cleanly with the online stack absent. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 21:02:28 +02:00
leonarski_fandClaude Opus 4.8	74c2c808de	cmake: drop GCC-only hardcoded flags, bump CUDA to C++20 ... Make the build less hostile to MSVC (needed for the viewer port) and align the CUDA standard with C++. - Remove the CMAKE_C/CXX_FLAGS_RELEASE overrides: -O3/-DNDEBUG only duplicate CMake's own GCC/Clang Release defaults, and the SET() clobbered the MSVC defaults. The lone meaningful flag, -Wno-deprecated-enum-enum-conversion, merely silenced warnings from the vendored Xilinx ap_private.h in the FPGA path; with no -Werror it is just log noise, so drop it. - CMAKE_CUDA_STANDARD 17 -> 20 (+ STANDARD_REQUIRED); CUDA >= 12.8 already supports C++20. - Drop the file-scoped -Ofast on JFPedestalCalc.cpp / JFConversionFloatingPoint.cpp: it is GCC-only and reaches the MSVC viewer via JFJochCommon -> JFCalibration. Those files now build at plain -O3. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 21:02:28 +02:00
leonarski_f	1e53db8f64	Docker: Update 2606 to support python3.12/3.13	2026-06-19 20:56:13 +02:00
leonarski_fandClaude Opus 4.8	3ce7666738	make_doc.sh: prefer the newest available python3.x ... The bare python3 is often too old for the Sphinx build. Auto-select the newest python3.13/3.12/3.11/3 found on PATH, still allowing $PYTHON to override. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 16:37:32 +02:00
leonarski_f	4e9505e6bb	make_doc.sh: Use python3	2026-06-19 16:06:49 +02:00
leonarski_fandClaude Opus 4.8	a34a033c99	frontend: auto-fill the missing phi bound for a sector ... When only one azimuthal phi bound is entered, fill the other so the sector is well-defined and the server accepts it: a missing phi_min becomes 0 and a missing phi_max becomes 360. Leaving both empty still means a full ring. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 16:05:15 +02:00
leonarski_fandClaude Opus 4.8	e9e5ec79cd	frontend: phi_min/phi_max columns in the azimuthal ROI table ... Surface the optional azimuthal phi-sector bounds (phi_min_deg/phi_max_deg) as editable columns, so a sector can be set from the web UI, not only the viewer. Also fix the Q_max row's d header, which read d_max but is d_min. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 16:01:13 +02:00
leonarski_fandClaude Opus 4.8	e60b42ea83	viewer: white, compact, right-aligned ROI numeric fields ... The ROI bound editors now have a white background, a capped width and right-aligned text, which reads better for numeric entry. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 16:01:13 +02:00
leonarski_fandClaude Opus 4.8	abc1d1c079	viewer: add/subtract the selected ROI to/from the user mask ... Restore the ROI-to-mask action on the new list: "Add to mask" and "Subtract from mask" buttons rasterise the selected ROI into the user mask (set or clear), through the same UpdateUserMask_i path. The ROI is evaluated with per-pixel resolution and phi from the geometry, so box, circle and azimuthal (sector) ROIs all map correctly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 15:08:59 +02:00
leonarski_fandClaude Opus 4.8	81b48febcf	viewer: remove the dead scratch-ROI widgets and worker methods ... With the scratch ROI panel gone, delete the now-orphaned JFJochViewerImageROIStatistics(_Box/_Circle) widgets and the worker's unused scratch-ROI plumbing (SetROIBox/SetROICircle, the ROIElement member, AddROIToUserMask/SubtractROIFromUserMask). ROI-to-mask, if wanted later, should act on the selected list ROI. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 14:58:33 +02:00
leonarski_fandClaude Opus 4.8	52aca9a4a9	docs: ROIs/azimuthal apply to both FPGA and DECTRIS workflows ... Clarify in FPGA_DATA_ANALYSIS.md that the ROI and azimuthal definitions are also evaluated on CPU via the shared image_analysis library, so they apply to the DECTRIS SIMPLON (EIGER) path that has no FPGA, not only the FPGA-accelerated JUNGFRAU/PSI path. Document the three NXmx writer formats (Legacy/VDS/Integrated) and the two acquisition workflows in CLAUDE.md. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 14:55:01 +02:00
leonarski_f	d4c96d48fc	make_doc.sh: Use default python	2026-06-19 14:52:40 +02:00