e7edee6b2ed5bc6a384eea421ced4dc28e911087
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Commits
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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> |
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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> |
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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> |
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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> |
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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>
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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> |
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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> |
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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> |
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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>
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9c417d322f |
viewer: dock the processing panel next to the plots; HTTP-mode notice
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- 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> |
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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> |
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74f36710e4 |
viewer: converge processing settings into one tabbed window + Bragg/scaling
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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> |
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5bfa70c4a6 |
viewer: Processing jobs window - run jfjoch_process in-GUI + result snapshots
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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> |
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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> |
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d14b8e9e18 | Merge upstream | ||
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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> |
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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> |
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c49bd2ac3b |
v1.0.0-rc.152 (#62)
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* jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5) * jfjoch_viewer: Adjust Q bounds for azimuthal integration * jfjoch_azint: Add tool to do quick azimuthal integration Reviewed-on: #62 |
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100fe7b7e7 |
PixelRefine: make factored Terms 1+2 the model, remove old wiring
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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> |
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c8db50ab41 |
jfjoch_viewer: missing pixel refine table
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d31063ca3f |
PixelRefine: Some improvements
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efe882f4b6 |
jfjoch_viewer: Better display (to be tested) of pixel refine
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6af22b6a0c |
jfjoch_viewer: show image CC based on standard pipeline
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003fea1b1e | jfjoch_viewer: fix sorting by indexing status | ||
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2d202f1d44 |
jfjoch_viewer: fixes to pixel refine window
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feca63f4b9 |
jfjoch_viewer: fixes to pixel refine
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8a582b8a90 |
JFJochMagnifierWindow: Fixed
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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 | ||
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e4b66f9cd9 |
PIxelRefine: Another iteration
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05711a1077 |
jfjoch_viewer: Add pixel refinw and magnifier windows (to be tested)
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cc3eb8352c |
v1.0.0-rc.148 (#58)
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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 |
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75de40f52b |
v1.0.0-rc.147 (#57)
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This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_viewer: Add reciprocal space viewer * jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset * jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress) Reviewed-on: #57 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> |
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fc68a9baed |
v1.0.0-rc.146 (#56)
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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 |
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c981e1b91c |
v1.0.0-rc.137 (#46)
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This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Better track time for each operation in the processing stack * jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress) * jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress) * jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0) Reviewed-on: #46 |
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1ab257af6c |
v1.0.0-rc.125 (#32)
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This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> |
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9bc71cfddc |
v1.0.0-rc.111 (#17)
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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> |
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224cc8b89c |
v1.0.0-rc.110 (#16)
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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> |
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05410d7cb3 |
v1.0.0-rc.109 (#15)
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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> |
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95acf3aba3 |
v1.0.0-rc.104 (#9)
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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> |
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808691251e |
v1.0.0-rc.101 (#6)
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This is an UNSTABLE release. * jfjoch_viewer: Auto load is better handling change of states * jfjoch_viewer: Fix DBus registration * jfjoch_viewer: Handle charts better with vertical lines on hover and status bar update * jfjoch_viewer: Calculate ROI in a more efficient way Reviewed-on: #6 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> |
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4dbbf0e365 |
v1.0.0-rc.97
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This is an UNSTABLE release and not recommended for production use (please use rc.96 instead). * jfjoch_broker: For DECTRIS detectors add dark data collection during initialization for bad pixel mask * jfjoch_broker: Refactor of calibration logic for more clear code (likely to introduce problems) * jfjoch_viewer: Add option to handle user pixel mask (experimental) * jfjoch_viewer: More options for ROI * jfjoch_viewer: Add window to display calibration Reviewed-on: #2 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> |
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