13 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Fable 5	53d6aa4ddf	viewer: ring labels that stay in view, and an inspector that reads at a glance ... The resolution-ring label was placed at one of four fixed azimuths with its corner on the ring line, in a hardcoded 16 pt Arial, in the ring's own magenta: it clipped at the viewport edge, ignored the font size, and vanished into busy patterns. It now walks the ring's cached trace, centres on the first point where the whole text fits in the viewport (failing that, clamps the nearest visible point inside), keeps a constant on-screen size of 1.2x the application font, and is cased like the spot markers so it reads on any colour map. In the same function visibleRect now maps viewport()->rect(), which is what mapToScene expects. The dataset plot's angle axis snaps its ticks to round angles - multiples of 90 degrees when the sweep is wide enough - instead of whatever angle the evenly-spaced image ticks landed on. The inspector prints the indexed cell as two aligned rows (alpha below a, beta below b, gamma below c), mosaicity with two decimals, and "No lattice" in grey, keeping red for actual trouble. The armed "Analyze image" button stays navy and is marked by a coral outline instead of turning into a differently-coloured button. The dataset navigation keys leave the image's keyPressEvent - the window-wide filter of the previous commit sees them first. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015vRwzF8PLaaa2novAKYorq	2026-09-13 20:20:54 +02:00
leonarski_fandClaude Opus 5	0ca6b251e5	jfjoch_viewer: no settings section is wider than the panel it sits in ... Measured every section's content minimum width against the 330 px the settings dock gives it (the powder one, fixed yesterday, sat at 278): geometry 346, unit cell 355, goniometer 322, spot finding 370, indexing 321, bragg 287, scaling 297, azint 243, reference 149 Five over. Three causes, none of them about the section: - addRow("", w) reserves the label column and puts the widget in the field column, so a checkbox's whole width was added to the widest label. addRow(w) spans both columns instead, which is what a label-less row means anyway. Spot finding 370 -> 251. - A spin box is never narrower than its longest possible value, suffix included, and these rows hold two or three abreast. The unit moves to the row label, which is how the panel names units elsewhere ("High resolution [Å]"): "a, b, c [Å]", "Beam origin [px]", "Detector tilt [°]", "Step x, y [μm]", "Radii r1/r2/r3 [px]". A cell length can still be four digits and three decimals, so those six fields also divide the row rather than demand their own width. - A combo is never narrower than its longest entry - the same thing that pinned the powder panel. "Flex (best per-image refinement)" set the indexing section's width; it elides now, as the calibrant does. Every section is now 291 or less, and none of them moves the dock. Two inspector changes in the same panel: - An axis that is present but does not turn covers no angular range, so the image angle is stated as one number rather than "-145° + 0°". - Sample-head angles that stay put during a run - an SLS Smargon writes chi and phi - get a row of their own, "chi 0° / phi 0°". Both its labels stay empty for a file that carries none, so it costs nothing where it means nothing. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011oVDk7aukYqfPZBLHn5nGg	2026-09-12 07:31:54 +02:00
leonarski_fandClaude Opus 5	a7a4c28925	jfjoch_viewer: the inspector states the numbers it used to hide ... Six changes to the desktop viewer, all in what it shows and what it is called: - The left-hand reprocessing panel is titled "Processing" (it sits next to "File manager"); the jobs panel that held that name is "Jobs". - The file manager lists *.cbf beside the HDF5 datasets. A CBF is one frame per file and opening any of them opens its sweep, which is what the File > Open dialog already did. - Image statistics: collection time, detector distance, beam centre and wavelength were in the dataset row's tooltip, where a number nobody hovers over is a number nobody reads. They are rows of their own, in the order a person asks for them - what the dataset is, how it was collected, then what this image contains. Source/instrument and sample are bold like every other value. The B-factor row is gone. - A "Spots + background" plot: spot count on the left axis, background per pixel on the right, since a common scale would flatten one of them. The axis labels take the colour of their line - a legend costs exactly the vertical room those labels need at this dock height. It is what a live (HTTP) connection selects by default, until the user picks something else. - Expanding the powder-calibration section no longer widens the settings panel past the space it has. Two buttons side by side cannot be narrower than both their labels, and a combo is never narrower than its longest entry - a 40-character cell in the calibrant list set the minimum width of the whole dock. One button per row, the cell in a tooltip, and both combos allowed to elide. - The grid/per-image toggles both rebuild the metric selector now. The grid button did not, so leaving per-image mode through it left the per-image plot types listed - X-ray fluorescence offered as a metric of a grid scan - and their values were then read as per-dataset metrics. Each mode also remembers its own selection instead of carrying an index across two unrelated lists. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011oVDk7aukYqfPZBLHn5nGg	2026-09-11 22:07:54 +02:00
leonarski_fandClaude Sonnet 5	d24cdfcff4	jfjoch_viewer: navigation keys, one-shot auto-contrast, file manager panel, cleanup ... * Dataset-info plot hover shows a horizontal crosshair alongside the existing vertical one, so a run of hovers reads as a level or a drift at a glance. * `A` applies auto-contrast once instead of switching on persistent Auto mode (a new `oneShotAutoForeground()`, distinct from the toolbar's Auto toggle); pressing it a second time on the same image switches Auto on for good, and pressing it while Auto is already on leaves it on. The value itself comes from one `AutoForegroundValue()` shared with the continuous Auto path. * `Home`/`End`/`Page Up`/`Page Down` navigate the dataset (first/last image, one image forward/back); claimed in the diffraction view's keyPressEvent before QGraphicsView's default handling, which otherwise eats them to scroll the viewport. * Alt+wheel dataset navigation is removed - some window managers already took it before the app ever saw it, per the caveat that used to sit next to its entry in the shortcuts list. * The image strip dock and its dedicated thumbnail-rendering machinery in the reading worker (SetThumbnail*, RenderThumbnail_i) are removed; it cost a lot and nothing else used any of it. * Toolbar text: "Colour" -> "Color". * Color map, Auto and HDR mode now persist across sessions, the same way the window layout already does. * The Inspector's "Dataset:" path wraps at '/' (a zero-width space after each one) instead of being cut off when it doesn't fit one line. * LoadFile no longer reopens an already-open file - it forwards straight to LoadImage instead - which was the likely cause of a D-Bus client's per-image navigation lagging behind the same navigation done via the grid-scan hover. * New file-manager dock (left, tabbed with Settings via tabifyDockWidget): a directory tree filtered to *_master.h5/*_process.h5, rooted at JUNGFRAUJOCH_DATA_ROOT if set, else the last-browsed root, else the home directory. Most beamline users care about opening images, not reprocessing settings, so it's the tab raised by default. Its filter box narrows files only - a directory always passes - because filtering the directories too hid the matching files under any directory whose own name did not match, and hid the root's ancestors, which left the tree with no valid root index until the root was set again by hand. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PogHY7bWXV4bpctDPdyuDN Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-11 18:45:20 +02:00
leonarski_f	54c0100e8e	v1.0.0-rc.157 (#67) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-11 07:19:11 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00
leonarski_f	4878318c27	v1.0.0-rc.139 (#49) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start` * jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start' * jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time * jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received * jfjoch_broker: Use nanoseconds internally for frame/image/readout time * jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished) * jfojch_broker: Improve profiling of different data analysis steps * jfjoch_broker: Record integration reflection count * jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds) * jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked * jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets **Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time. Reviewed-on: #49	2026-04-29 09:50:50 +02:00
leonarski_f	27496b8207	v1.0.0-rc.122 (#29) ... This is an UNSTABLE release. * jfjoch_broker: Add thresholding to prefer shorter vectors after FFT * jfjoch_broker: Add experimental mosaicity estimation for rotation experiments (this is work in progress) * jfjoch_viewer: Display file opening errors * jfjoch_viewer: When loading files over DBus add retry/back-off till the file is available Reviewed-on: #29 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-16 15:27:40 +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	31a357fa57	v1.0.0-rc.113 (#19) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_broker: Improve handling of rotation indexing * jfjoch_broker: More information saved in CBOR end message (WIP) * jfjoch_writer: Save rotation indexing lattice parameters and Niggli class * jfjoch_viewer: Remove (for now) primitive cell information Reviewed-on: #19 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-02 09:29:22 +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	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