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Author	SHA1	Message	Date
leonarski_f	e7edee6b2e	viewer: Phase 1c — fold per-image plot into the dataset-info dock ... Remove the duplicated per-image plot from the side panel and host it in the dataset-info dock instead: - JFJochViewerDatasetInfo gains a "Per-image" toggle (next to Grid) that swaps the stacked view to the existing JFJochViewerSidePanelChart (azimuthal 1D, Wilson, I/sigma, spot and fluorescence profiles of the current image). The per-dataset metric combo is disabled while in per-image mode. - The per-image profile follows the displayed image (imageLoaded forwarded). - Drop the "Image statistics plot" section from JFJochViewerSidePanel. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-23 16:26:15 +02:00
leonarski_f	54526300a9	viewer: promote Reanalyze image / Reanalyze dataset hero buttons ... The two capabilities that set Jungfraujoch apart get prominent, paired navy buttons at the right of the display toolbar, with purpose-drawn icons (a single diffraction frame vs a stack of frames): - "Reanalyze image" re-runs the analysis pipeline on the current image (worker Analyze). - "Reanalyze dataset" opens a new whole-dataset processing job (JFJochProcessingJobsWindow::newJob, now public). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-23 16:26:15 +02:00
leonarski_f	9f9e13a4e4	viewer: PSI logo + tidy beam-center row ... - Show the PSI logo in the menu-bar corner, picking one of four interchangeable dot designs at random each launch. Embedded as PNGs (rasterised from the SVG sources, kept alongside) so no Qt SVG module dependency is needed. - Settings dock: put beam center X and Y on a single "Beam center" row to save vertical space on laptop screens. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-23 16:26:15 +02:00
leonarski_f	58c60e03fe	viewer: Phase 1b — inline MX/AzInt settings dock ... Surface a surgical subset of processing settings in an always-visible dock instead of hidden windows: - New JFJochViewerSettingsDock with an MX / AzInt segmented toggle. MX page: geometry (energy, distance, beam X/Y), a new unit-cell + space-group editor (no such input existed before; enables known-cell ffbidx), spot finding (S/N, photon count, min pixels/spot), indexing algorithm and geometry refinement. AzInt page: q range / spacing / azimuthal bins plus the existing powder-calibration widget. - Edits feed straight into the worker (UpdateSpotFindingSettings, UpdateAzintSettings, UpdateDataset, FindCenter); fields populate from the loaded dataset. - Add CeO2 and Silicon calibrant presets. - Dock it left, objectName "settingsDock", show it in the Processing perspective (hidden in Image). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-23 16:26:15 +02:00
leonarski_f	f5a146d212	viewer: Phase 1a — dockable shell with saved perspectives ... Make the layout reconfigurable, the foundation for the redesign: - The diffraction image becomes the central widget; the right-hand side panel is now a dockable "Inspector" (QDockWidget, right area). - Every dock and toolbar gets a stable objectName so QMainWindow saveState / restoreState round-trips. Dataset-info docks are numbered uniquely. - Persist geometry + dock state to QSettings on close and restore on launch, so the user's arrangement resumes. - New "View" menu with Image / Processing perspectives (show/hide the bottom plots + jobs panel) and "Reset layout" (back to the as-built arrangement, captured at startup). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-23 16:26:15 +02:00
leonarski_f	ecc06d9abd	viewer: Phase 0 redesign — slim headers, navy accent, icon nav ... First pass of the viewer redesign (see docs/review/VIEWER_REDESIGN.md), no structural change: - TitleLabel: replace the 50px solid #FA7268 section bars with a slim 26px navy-bold header + coral accent rule, removing the "venetian blind" stack while keeping the salmon identity. - Palette: switch the accent (QPalette::Highlight) from teal to navy #1F3A5F. - Image toolbar: replace the unicode arrow glyphs (|<= <= => =>|) with flat media icons (first/prev/next/last) + tooltips, and a play icon on Movie. - Bottom dock: give the per-dataset plot more default height (340 -> 420). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-23 16:26:15 +02:00
leonarski_f	68f3394f48	deps: pin external Eigen to 3.4.x across docs and Docker images ... Eigen is an external find_package(Eigen3 3.4) dependency. Eigen's same-major-version rule means a bare 3.4 request only accepts 3.x, so 5.x cannot be used without changing every requester (jfjoch, Ceres, and the upstream ffbidx). Standardise on Eigen 3.4.x: - docs: correct the Windows Eigen install recipe to 3.4.0 and note the same-major constraint; SOFTWARE.md now says 3.4.x (not "3.4 or newer"). - docker/{rocky8,rocky9,ubuntu2204,ubuntu2404}: actually install Eigen 3.4.0 from source to /opt/eigen-3.4 (header-only) and add it to CMAKE_PREFIX_PATH. The images previously installed no Eigen at all, relying on the obsolete "CMake fetches it" assumption; a rebuild would have failed at configure. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-22 20:53:42 +02:00
leonarski_f	ad5662732d	windows: auto-detect nvcc and drop manual CUDA/zlib flags ... Locate nvcc via find_program (HINTS CUDA_PATH / /usr/local/cuda) before CHECK_LANGUAGE(CUDA), so CMAKE_CUDA_COMPILER no longer has to be passed by hand. CHECK_LANGUAGE only searches PATH, which is missed routinely on Windows and intermittently on Linux; the CUDA installer always sets CUDA_PATH. An explicit -DCMAKE_CUDA_COMPILER / $CUDACXX still wins. Docs: zlib and Eigen are external find_package deps (not auto-fetched); simplify the Windows configure to just CMAKE_PREFIX_PATH (no CMAKE_CUDA_COMPILER, no ZLIB_ROOT); fix the Eigen 5.0.1 install recipe to disable BLAS/LAPACK (they fail MSVC with C1128 /bigobj) and use cmake --install. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-22 19:47:01 +02:00
leonarski_f	5f3126e19e	CMake: Update FFBIDX to support MSVC	2026-06-22 17:51:57 +02:00
leonarski_f	9defbffa67	Revert "CI: reuse jfjoch_hdf5_test via artifact in dials-test" ... This reverts commit 94125bd6cb.	2026-06-22 17:49:38 +02:00
leonarski_f	961836837f	viewer: salmon group boxes; dataset-info x-axis spans the whole dataset ... - Fusion fills QGroupBox interiors with a flat light colour, so the settings window lost its salmon look. A tiny app stylesheet (QGroupBox { background: transparent }) makes them show the salmon window background again; entry widgets stay white via the palette. - The dataset-info chart now fixes the x-axis to the whole dataset [0, n) (the largest run = the original file), so a subset run is drawn at its real image positions instead of being stretched to fill the plot. Subsets with binning bin by ordinal and place each point at its mapped image number (correct for the common contiguous sub-range). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 16:56:18 +02:00
leonarski_f	94125bd6cb	CI: reuse jfjoch_hdf5_test via artifact in dials-test ... Build jfjoch_hdf5_test once in a new build-hdf5-test job and hand the binary to dials-test as an artifact, instead of recompiling it from scratch in every rocky9 processing job. Uses the christopherhx gitea-{upload,download}-artifact fork (mirrored under gitea.psi.ch/actions) to avoid the stock v4 action's GHESNotSupportedError. Probe scope: dials-test only; xds-* still self-build until the round-trip is confirmed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 16:08:48 +02:00
leonarski_f	c86beeb393	rotation indexer: fix sub-range crash, explicit angle, settings + guards ... Running rotation indexing on a sub-range (e.g. images 60-120) segfaulted: the first pass passed the *global* image number to RotationIndexer::ProcessImage, which indexes v_ (sized to the run's image count) -> out-of-bounds write. - ProcessImage now takes an explicit mid-exposure angle (optional; falls back to the goniometer at the image index), so the indexer no longer assumes its slot index equals the goniometer image index. IndexAndRefine supplies it via RotationAngle(), matching the angle used for prediction. Added a bounds guard in ProcessImage so a bad index can never corrupt memory. - JFJochProcess feeds the rotation indexer the local ordinal (not the global index), and shifts the goniometer (start += start_image*incr, incr *= stride, per-image wedge preserved) so local index i maps to the angle of original image start+i*stride - fixing rotation angles for the whole sub-range pipeline (prediction, refinement, output), not just the indexer. - Expose "Rotation images" (number used for the first pass) in the job dialog, enabled when rotation indexing is on. (Count > available is already clamped by select_equally_spaced_image_ordinals.) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 15:59:21 +02:00
leonarski_f	67ad43a2b2	viewer: palette theming, Original as a run row, stable plot colours ... Styling (now via the application palette in main(), not a stylesheet, so it applies to every widget incl. dialogs): - Entry fields and item views (line edits, spin boxes, combos, tables) are white when enabled and salmon (the GUI default) when disabled - so it's clear where you can type. Panels stay salmon (Window role). - Teal (#2a9d8f) accent via the Highlight role: selections and progress-bar chunks. Runs list / plots: - The original file is listed as a first "Original" run (Mode "HDF5"); double-click any run row to show it (replaces the "Show original" button). The currently shown run is bold (driven by snapshotsChanged). - Fix the colour "swap" when switching runs: the primary line is matched by the active-dataset pointer (not active_id_), so a run keeps its colour even while a datasetLoaded/runsChanged pair is mid-flight. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 15:34:06 +02:00
leonarski_f	95fe2ce781	CI: Sign RPMs on upload	2026-06-22 15:22:21 +02:00
leonarski_f	03a09c43bc	viewer: white-when-active inputs, teal accent, Status column visible ... Styling: - Entry widgets (line edits, spin boxes, combos, item views) are salmon (the GUI default) when inactive and turn white while focused/active. - A teal accent (#2a9d8f) for selections and the QProgressBar chunk, against the salmon background. - Move the jobs-table Status column (the progress bar) to column 2 so it stays visible in the narrow dock instead of scrolling off the right edge. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 15:10:36 +02:00
leonarski_f	0f3009069f	viewer: processing dialog takes start + end image, not a count ... Replace the ambiguous "Images" count with explicit "Start image" and "End image" spinboxes (end 0 = to the last image). buildConfig sets config.start_image / end_image; the table shows the range ("start-end" / "all") and the progress bar expects end-start images. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 15:01:25 +02:00
leonarski_f	b9f8c2b675	reader/viewer: snapshot image->original map; subset runs register and overlay ... Foundation for a dataset (snapshot or, later, the main file) being a subset of the truly collected images: - JFJochReaderDataset gains source_image_number (image index -> original image number; empty = identity). - HDF5MetadataSource reads /entry/detector/number into that map and an inverse (original -> local) map; FillPerImage / ReadSpots translate the requested global image to this source's local index via ToLocalIndex (return nothing if the image is not covered), so partial snapshots are correct and never read out of bounds. - RegisterSnapshot now accepts a snapshot with fewer images than the dataset (only rejects more), so sub-range / strided reprocessing runs register. - The dataset-info plot draws each run at its original image numbers (x map from source_image_number), so a subset run lands at the right place on the shared axis. The live run's map is filled from msg.original_number. This makes the foundation ready for strided / filtered selections (e.g. reprocess only images with >N spots) without restricting to a min-max sub-range. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 14:59:23 +02:00
leonarski_f	7ba097df1c	viewer: looser minimum heights so the bottom docks resize freely ... Lower the dataset-info chart and jobs-table minimum heights (200 -> 80, table 60) so the bottom dock area can be dragged smaller; the comfortable default size is still set via resizeDocks. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 12:24:47 +02:00
leonarski_f	a412f96f3a	viewer: give the current-image plot marker a fixed colour ... The current-image marker (a scatter series) was picking an arbitrary theme colour (green), which read as a stray series. Pin it to black so it's an unambiguous "current image" dot, distinct from the run line colours. Its legend entry is already hidden. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 12:13:39 +02:00
leonarski_f	2af822436e	viewer: remove/clear runs, stable per-run colours, processing rate + ETA ... - "Remove result" toolbar action drops a reprocessing run: reader RemoveSnapshot (Original is protected; if the removed run was active the view falls back to Original), worker RemoveRun, and the table row is removed. - Opening a new file clears the jobs table (worker fileOpened -> clearJobs) to match the reader, which already resets snapshots on ReadFile. - Plot fixes: each run keeps a stable colour by its position (Original = blue), so colours no longer swap when the active run changes; the current-image marker is hidden from the legend (was the stray "[Image #N]" entry). - The status bar shows processing rate (Hz) and estimated remaining time while a job runs. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 12:00:15 +02:00
leonarski_f	aceff23ce2	viewer: overlay one plot line per processing run (with editable names) ... The dataset-info plot now overlays every run as a separate named line instead of replacing the plot when a snapshot is activated: - Reader gains AllSnapshotDatasets() (every snapshot's dataset, Original first). - The worker owns the run collection: a stable snapshot id plus an editable display label (RunData), emitted as runsChanged(runs, active_id) on file open, snapshot register, activate and rename. RenameRun(id, label) updates the legend label without touching the reader key (decoupled id vs label). - The chart view draws the active run as the primary series (markers, hover, binning, axes) and the other runs as overlay lines sharing its axes, with a legend shown when overlaying (appendSeries factored out for both). - The dataset-info widget holds the run list + the live run, extracts the selected metric from each (ExtractMetric), and unions the available metrics across runs. - The live run is its own "Live" overlay (lightweight per-tick refresh, no combo rebuild); it is cleared on finish so the persisted snapshot takes over. - The processing jobs table gets a "Started" column and an editable Name column; editing a name renames that run's legend label. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 11:28:47 +02:00
leonarski_f	b735aec1c4	viewer: show effective indexing algorithm; disable GPU options without CUDA ... - The Indexing tab now shows what the selected algorithm resolves to on this machine/dataset ("Effective on this system: ..."), mirroring DiffractionExperiment::GetIndexingAlgorithm() so Auto is no longer ambiguous (GPU present? unit cell known?). Cell-known state is forwarded from the loaded dataset via JFJochSettingsWindow::datasetLoaded. - FFBIDX and FFT (GPU) radio options are disabled on builds without CUDA, where only the FFTW CPU indexer exists. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 11:09:21 +02:00
leonarski_f	42219d8c5b	viewer: fix bottom-dock height, window size, and snapshot-switch lag ... Regressions from docking the processing panel + live plots: - Default window size is now screen-aware (fits a laptop) instead of a fixed 1200x1200. - Give the bottom dock area a guaranteed height (resizeDocks vertical) and a minimum height on the dataset-info chart, so the plot and its axis labels stay visible next to the processing panel. - Activating a metadata snapshot (Show original / View results) no longer re-runs full analysis: it re-reads the image against the snapshot's stored results with reanalysis suppressed, instead of re-indexing on every switch. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 09:58:51 +02:00
leonarski_f	9c417d322f	viewer: dock the processing panel next to the plots; HTTP-mode notice ... - Convert JFJochProcessingJobsWindow from a standalone helper window into a dockable QWidget panel (toolbar + stacked table/message), placed in the bottom dock area and split horizontally to sit in the bottom-right corner next to the dataset-info plots. Its show/hide toggle moves to the Window menu via the new JFJochViewerMenu::AddDockEntry. - When connected to a live HTTP stream the panel shows "Dataset re-processing is currently available only in File mode" and disables the toolbar, driven by the worker's httpConnectionChanged signal. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 08:35:56 +02:00
leonarski_f	940b7e34d4	viewer: indexing algorithm/refinement radio groups, rotation fix, live job plots ... Processing settings: - Split the spot/index settings widget into two tabs (Spot finding | Indexing) via TakeSpotFindingPage()/TakeIndexingPage(). - Indexing tab now exposes the indexing algorithm (Auto/FFBIDX/FFT/FFTW/None) and geometry refinement (None/Orientation/Beam center/Pixel refine) as radio groups with short explanations. - Fix: UpdateSpotFindingSettings dropped algorithm + geometry-refinement when copying into indexing_settings (the geom checkbox was a no-op); both now flow into jobs via curr_experiment. Processing jobs window: - Rotation indexing from the job dialog now also sets RotationIndexing(true) on the experiment's IndexingSettings; otherwise IndexAndRefine builds no rotation indexer and the two-pass pre-pass throws. - Status cell shows a QProgressBar with "<done> / <expected>". - Live results: JFJochProcessController::OnImageProcessed accumulates per-image results into a JFJochReaderDataset and emits it throttled (~4 Hz) as liveDataset, forwarded to the dataset-info plots so they update while a job runs. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-22 08:30:49 +02:00
leonarski_f	95223fc281	CI: Tests needs LFS to get rotation dataset	2026-06-22 07:17:31 +02:00
leonarski_f	74f36710e4	viewer: converge processing settings into one tabbed window + Bragg/scaling ... One "Processing settings" window with tabs: Spot finding & indexing | Azimuthal | Bragg integration | Scaling, replacing the two separate settings windows. The spot/index and azimuthal tabs reuse the existing windows' widgets unchanged (their content is lifted into tabs via takeCentralWidget), so all their logic/signals keep working; Bragg integration and scaling are new editable panels (previously not adjustable in the GUI). JFJochImageReadingWorker gains UpdateBraggIntegrationSettings / UpdateScalingSettings; both persist as worker state and are re-imported into curr_experiment on file load / dataset update (like the indexing/azint settings), so they apply to interactive analysis (Bragg) and flow into processing jobs via GetReprocessingInputs (Bragg + scaling). Scaling only affects the job post-pass, so it is just stored, not reanalyzed. Verified: jfjoch_viewer builds and runs (offscreen) with the converged window. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 17:09:20 +02:00
leonarski_f	c916cf8b2d	tests: drop the serial [large] test (serial dataset not shipped) ... Only the ~1800-image rotation dataset is kept in LFS; a separate ~5000-image serial set is too large to ship, and the serial path can be exercised by running the rotation series in serial mode if needed. Removes JFJochProcess_LysoSerial and the serial entry from the start-up listener and README. The rotation [large] test now runs against the committed data and passes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 16:46:56 +02:00
leonarski_f	ed8fb5d37c	tests: add lyso rotation dataset (1800 images) via git-LFS ... Real reference dataset for the [large] JFJochProcess_LysoRotation test, stored with git-LFS (tests/data/*.h5). lyso_rotation_master.h5 is the 1800-image lysozyme rotation series (its data files keep the names the master links to). The test indexes it at 100% with cell ~78.2/78.2/37.8; it SKIPs when the data is not pulled. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 16:05:25 +02:00
leonarski_f	5bfa70c4a6	viewer: Processing jobs window - run jfjoch_process in-GUI + result snapshots ... Makes the viewer a processing frontend, not just an image viewer: - JFJochProcessingJobsWindow (menu "Processing"): a table of processing jobs on the open dataset. "New job" configures mode (full/azint), image count, threads, output, and (full) rotation indexing + scale/merge, using the viewer's current processing settings. A job can be Run locally (off the GUI thread via JFJochProcessController, with live status/progress and Cancel) or its jfjoch_process command line copied for a cluster. - A finished local run is registered as a reader metadata snapshot and becomes the active dataset (bottom plots + per-image overlays follow it); "View results" / "Show original" switch between runs - so several settings attempts on one dataset can be compared. - JFJochImageReadingWorker gains GetReprocessingInputs() (one locked read of file + experiment + mask + spot-finding settings, so jobs share the interactive settings) and RegisterProcessingSnapshot/SetActiveSnapshot slots + snapshotsChanged signal over the reader's snapshot API. Files only (not live HTTP). First-cut / open ends: one job at a time; output lands in the working dir (FileWriter rejects absolute prefixes); Bragg/scaling settings still use defaults until the converged settings window lands. Viewer builds and runs (offscreen) cleanly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-21 14:38:17 +02:00
leonarski_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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_f	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