32 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	142cb88aa8	viewer: shift/ctrl-drag creates list ROIs; remove the old scratch panel ... The interactive shift-drag (box) / shift+ctrl-drag (circle) now creates a new persistent ROI in the list instead of feeding the old single-ROI scratch panel. The base emits a roiScratchDrawn hook on release; the diffraction image turns the drawn shape into a named ROI committed via SetROIDefinition. The old JFJochViewerImageROIStatistics scratch panel and all its wiring (box/circle configuration, single-ROI result, add/subtract user mask) are removed from the side panel and window; the ROI list is now the single source. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 14:31:23 +02:00
leonarski_fandClaude Opus 4.8	d413af0e92	viewer: azimuthal ROI handles, and keep panning inside the ROI ... Azimuthal ROIs now show discrete grab handles on the selected ROI: the inner/outer arc (resize Q/d) and, for a sector, the two phi edges (rotate). Editing is by clicking a handle, with a generous tolerance, which fixes the previously near-impossible phi-edge grab. Clicking the (large) interior of an azimuthal ROI now only selects it and lets the view pan, instead of capturing the gesture. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 14:21:23 +02:00
leonarski_fandClaude Opus 4.8	00b58cd426	viewer: resize box/circle/azimuthal ROIs and delete with the Delete key ... Extend canvas ROI editing beyond move: - Box: drag corners/edges to resize (handles shown on the selected ROI). - Circle: drag the perimeter to resize, interior to move. - Azimuthal: drag the inner/outer arc to change the Q/d range, or a radial edge to rotate a phi bound; sampled through the geometry so it tracks the conic. - Delete removes the selected ROI (the view now takes keyboard focus). All edits go through the same live, throttled SetROIDefinition path. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 14:07:16 +02:00
leonarski_fandClaude Opus 4.8	d9dfd36413	viewer: click to select an ROI, with live move and a hand cursor ... Clicking a box/circle on the image now selects it (syncing the side-panel combobox) and grabs it for moving, with a closed-hand cursor during the drag. The move recomputes ROI statistics live rather than only on release, throttled to at most one in-flight recompute so the worker is not flooded. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	308265c7b1	viewer: move the selected box/circle ROI on the canvas ... Add base-class mouse hooks (roiEditPress/Move/Release) so the diffraction image can edit the persistent ROI selected in the side-panel combobox. The selected ROI is highlighted (dashed, thicker), and dragging its interior moves a box or circle; on release the new geometry is committed through SetROIDefinition, which recomputes only the ROIs. Resize, azimuthal handles and delete-key follow. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	2f8d486b51	viewer: ROI list panel — select, add, rename, delete, per-ROI results ... Add JFJochViewerROIList to the side panel: a list of the dataset's ROIs with selection, add (box/circle/azimuthal), rename and delete, plus a statistics readout (sum/mean/std/max/valid/masked/centre-of-mass) for the selected ROI, taken from the analysis output for the current image. Edits emit a full ROIDefinition, routed to the worker's SetROIDefinition. Per-ROI statistics now live in this panel rather than the canvas labels; the diffraction image's labels show only the ROI name, and the ad-hoc ROIIntegrationCPU computation there is removed in favour of the analysis pipeline. The result widget now reports std dev instead of variance. The single-ROI scratch panel remains for now and will be retired once the interactive canvas editing replaces it. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	3996595606	viewer: per-ROI statistics on the diffraction image via the CPU ROI engine ... When ROI labels are shown, each ROI's label now also reports its sum, max and pixel count for the current image. Rather than reimplementing the accumulation, this reuses the existing ROIIntegrationCPU engine (the software counterpart of the FPGA roi_calc), built from the experiment and cached per dataset. A small adapter folds the viewer's gap sentinel (INT32_MIN+1) onto the engine's masked sentinel (INT32_MIN) so masked and saturated pixels are handled correctly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	33118ebe8b	viewer: fix stray line from origin on full-ring azimuthal ROI ... The full-ring annulus built the inner ring as a separate QPainterPath and merged it with addPath, which stitched a spurious segment from (0,0) to the ring. Build both concentric rings as subpaths of one path, each begun with an explicit moveTo, so there is no connecting segment. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	7d6f79a1da	viewer: draw azimuthal ROI wedges, with optional fill and labels ... Azimuthal ROIs now render on the diffraction image as annular sectors (or full-ring annuli), sampled through DiffractionGeometry::ResPhiToPxl so the outline follows the ROI footprint, including wrap-around sectors. Add two side-panel toggles (both default off): a translucent fill for every ROI (helpful when outline colours clash with the image colour map, and with many ROIs) and ROI name labels (constant on-screen size). Wired side panel -> window -> diffraction image like the existing feature toggles. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	35f6ffdde9	viewer: draw loaded ROIs on the diffraction image ... When a file with ROI definitions is opened (read into experiment.ROI() by the HDF5 reader), the diffraction image now overlays the configured box and circle ROIs as distinct colour-coded outlines, alongside the existing resolution rings and spots. This is the first step of the ROI-map-based multi-ROI canvas: showing the ROIs loaded from a file. Azimuthal ROIs (wedge rendering) and per-ROI statistics from the bitmap follow in subsequent steps. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-19 13:56:09 +02:00
leonarski_fandClaude Opus 4.8	5d9e1be814	portability: replace M_PI / std::numbers::pi with a host+device-safe PI ... M_PI is a POSIX <math.h> extension that MSVC does not define without _USE_MATH_DEFINES. std::numbers::pi (introduced in the viewer guard commit) is C++20, but CUDA here is compiled as C++17 (CMAKE_CUDA_STANDARD 17) and several common/ headers are pulled into .cu device translation units, so std::numbers is not available there. Add common/JFJochMath.h with a dependency-free `constexpr double PI` that works in host code (including MSVC), in CUDA device code, and under C++17/20, and use it everywhere: - common/ and image_analysis/ (incl. CUDA .cu): 78 M_PI occurrences, 22 files - broker/OpenAPIConvert.cpp - viewer/: the 5 files that used std::numbers::pi now use PI, for one consistent convention across the codebase Verified to build: JFJochImageAnalysis (incl. CUDA), jfjoch_viewer, JFJochBroker. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-18 14:54:01 +02:00
leonarski_fandClaude Opus 4.8	ec1308f4a9	viewer: guard Linux-only constructs for Windows/MSVC builds ... Step toward building jfjoch_viewer on Windows/MSVC. No change to the Linux build: D-Bus stays on by default and the XCB plugin is still used. - CMake: make Qt6::DBus optional via JFJOCH_VIEWER_DBUS (ON on Linux, OFF on Windows/macOS where Qt6::DBus does not exist); compile/link/install the dbus/ adaptor + service file only when enabled. Select the platform integration plugin per-OS (QXcb on Linux, QWindows on Windows, QCocoa on macOS) instead of hard-coding QXcbIntegrationPlugin. - JFJochViewerWindow: wrap the adaptor include and D-Bus registration in #ifdef JFJOCH_VIEWER_DBUS. - JFJochImageReadingWorker: the POSIX open()/fstat()/NFS-errno preflight is now #ifndef _WIN32, with a portable QFileInfo fallback elsewhere; POSIX-only headers are guarded too. - Replace the POSIX M_PI/M_PI_2 extension with C++20 std::numbers::pi across the viewer (not defined by MSVC without _USE_MATH_DEFINES). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-18 13:50:49 +02:00
leonarski_fandClaude Opus 4.8	100fe7b7e7	PixelRefine: make factored Terms 1+2 the model, remove old wiring ... PixelRefine is now an intensity-only operation: geometry is fixed (refined upstream by XtalOptimizer) and the only objective is the factored per-reflection likelihood (FACTORED_MODEL.md Terms 1+2) - measured per-resolution profile width R1 plus one Fisher-weighted intensity/scaling residual per reflection, fitting the per-image scale G and B. Validated on crystal 2 (fixed_master.h5 as stills, 1.7 A): CC1/2 84-92%, CCref 77-92%, flat - reproduces the env-flag prototype and matches the rotation path from the stills path. Removed: - the per-pixel ShoeboxResidual loss and PixelResidual cost functor; - all in-PixelRefine geometry refinement (orientation/cell/beam/distance/R), the regularised-orientation LSQ, signal-weighting, and the global sweep; - Term 3 (per-spot recentring) - a confirmed no-op on both crystals; - the diagnostic scaffolding (covariance, centroid, adaptive_R1) and the PR_* env knobs + stderr dumps in IndexAndRefine; - the PredictImage/ChiSquaredImage renderers and the entire viewer PixelRefine window/table/params + worker bindings + shoebox overlay. The sweep box-integrator background median became mean (consistency) by virtue of removing the sweep. METHODS.md rewritten for the current model; findings recorded in FINDINGS-2026-06.md. Net -2200 lines. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-13 22:02:18 +02:00
leonarski_f	efe882f4b6	jfjoch_viewer: Better display (to be tested) of pixel refine	2026-06-09 16:28:17 +02:00
leonarski_f	2d202f1d44	jfjoch_viewer: fixes to pixel refine window	2026-06-09 13:20:46 +02:00
leonarski_f	8a582b8a90	JFJochMagnifierWindow: Fixed	2026-06-09 12:09:40 +02:00
leonarski_f	30dcc98f89	JFJochMagnifierWindow: Zoom is saved ... it is not optimal (when image is first loaded, than it starts with weird zoom), but can be fixed later	2026-06-09 12:03:45 +02:00
leonarski_f	05711a1077	jfjoch_viewer: Add pixel refinw and magnifier windows (to be tested)	2026-06-08 21:22:19 +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	2026-06-08 08:30:35 +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	2026-05-28 18:48:35 +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>	2026-04-16 11:59:59 +02:00
leonarski_f	07fe4dd3bb	v1.0.0-rc.124 (#31) ... This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. * jfjoch_broker: Improve refection position prediction and Bragg integration code. * jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. * jfjoch_writer: Fix saving mosaicity properly in HDF5 file. * jfjoch_viewer: Introduce high-dynamic range mode for images * jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) * jfjoch_viewer: Zoom-in numbers have better readability Reviewed-on: #31 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-01 13:29:33 +01:00
leonarski_f	1c4dfd03e2	v1.0.0-rc.123 (#30) ... This is an UNSTABLE release. * jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility * jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) * jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) * jfjoch_viewer: Add more color schemes for better image readability * HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable * HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists Reviewed-on: #30 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-01-30 13:43:09 +01:00
leonarski_f	e2b240356c	v1.0.0-rc.121 (#28) ... This is an UNSTABLE release. * jfjoch_broker: Report changes in the image buffer, so viewer doesn't reload constantly * jfjoch_viewer: Improve performance of loading images * jfjoch_viewer: Auto-throttle image loading in HTTP-sync / movie modes * jfjoch_viewer: Auto-foreground calculated with histogram * jfjoch_viewer: Fix rare segmentation fault Reviewed-on: #28 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-12 21:24:20 +01:00
leonarski_f	36d0507758	v1.0.0-rc.119 (#26) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_broker: Add binary export of data analysis plots over OpenAPI * jfjoch_broker: Minor fixes to HTTP error handling * jfjoch_viewer: Prefer binary plots over JSON plots * jfjoch_viewer: Change foreground with F button + wheel * jfjoch_viewer: Change way how angles are displayed * jfjoch_viewer: Display resolution of the mouse cursor in top left corner Reviewed-on: #26 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-08 19:53:35 +01:00
leonarski_f	9bc71cfddc	v1.0.0-rc.111 (#17) ... This is an UNSTABLE release. * jfjoch_viewer: Remove 3D lattice viewer (not really useful at this moment) * jfjoch_viewer: Fix auto contrast not refreshing image Reviewed-on: #17 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-28 16:22:18 +01:00
leonarski_f	224cc8b89c	v1.0.0-rc.110 (#16) ... This is an UNSTABLE release. * jfjoch_broker: Add auto-contrast option for preview images * Frontend: Add logo image * jfjoch_viewer: Add logo image * jfjoch_viewer: For image chart allow to set min value to zero * jfjoch_viewer: For resolution estimation plots, visualization uses 1/d^2 as measure * jfjoch_viewer: Add 3D unit cell visualization (experimental/WIP/not really there) * Documentation: Add logo image Reviewed-on: #16 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-28 12:47:35 +01:00
leonarski_f	05410d7cb3	v1.0.0-rc.109 (#15) ... This is an UNSTABLE release. * jfjoch_viewer: Add keyboard shortcuts and option to copy image to clipboard * jfjoch_broker: Fix bit-width and exposure time for PSI EIGER detectors Reviewed-on: #15 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-26 13:48:59 +01:00
leonarski_f	d53e93023b	v1.0.0-rc.108 (#13) ... This is an UNSTABLE release. * jfjoch_viewer: Fix bug when resolution estimation/B-Factor/Profile radius were not set (NaN) * jfjoch_viewer: Show spots is off by default, resolution ring mode is enabled by default * jfjoch_viewer: Fit to window of image is now default when size of the grid changes Reviewed-on: #13 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-24 12:27:54 +01:00
leonarski_f	ddcc24fba8	v1.0.0-rc.106 (#11) ... This is an UNSTABLE release. * jfjoch_viewer: Allow for multiple dataset info plots * jfjoch_viewer: Highlight current element in grid Reviewed-on: #11 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-21 11:03:29 +01:00
leonarski_f	a6b5cb5629	v1.0.0-rc.105 (#10) ... This is an UNSTABLE release. * jfjoch_viewer: Clean-up widgets slightly * jfjoch_viewer: Limit right panel to 600 pixels * jfjoch_viewer: Parse crystal symmetry type * jfjoch_viewer: Grid scan view takes color map and can be fit to zoom Reviewed-on: #10 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-20 09:46:25 +01:00
leonarski_f	95acf3aba3	v1.0.0-rc.104 (#9) ... This is an UNSTABLE release. jfjoch_writer: Fix and improve the way grid scan geometry is saved (non-NXmx extension makes it way easier) jfjoch_viewer: Display grid scan results in 2D (work in progress) jfjoch_viewer: Improve auto-scaling on start of images (work in progress) jfjoch_viewer: Add B-factor and resolution estimate to the dataset info plots Reviewed-on: #9 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-19 17:28:10 +01:00