104 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	16bf3408f0	Address code-review findings; make detection limits detector-driven ... One changeset, developed together in response to a review of this branch, so the files carry several of the changes at once. Full test suite passes (733 cases). Spot finding - Split ImageSpotFinder into Detect() (flag strong pixels - the expensive per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with Run() = both. The per-image min-pix escalation now detects ONCE and repeats only the cheap extraction, instead of re-running the whole finder four times per frame as it did on the default path. It also keeps the winning attempt's spot list rather than re-extracting it, so the frame that is integrated is exactly the frame that was scored - which a GPU re-extract could not guarantee (float atomic ordering). - spot_finding_time_s no longer swallows indexing time, and indexing_time_s now sums every escalation call instead of reporting only the last. Detection limits follow the detector - The azimuthal-integration upper q and the spot-finding high-resolution limit are now std::optional, in the C++ structs AND in the OpenAPI schema, and resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_ recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a pixel outside that q range could never be strong - the integration range silently bounded what detection could see, regardless of the requested resolution limit. Regenerated the C++ and TypeScript clients; the viewer and the web frontend each gained a "to detector edge" switch. Detection defaults are now per workflow (measured, not assumed) - Stills: adaptive detection, min-pix chosen per image, no resolution clipping. - Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit. On a 33-crystal rotation battery, adaptive detection helped four hard crystals but deterministically broke three (a lost space group, a halved indexing rate, a collapsed merge), and the detector-edge limit cost indexing on a strong rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and --no-adaptive-spots is new. Indexer seed escalation - Stop escalating once a seed's lattice explains >= 90% of the seed spots. Previously any frame with >= 80 spots always paid three indexer calls, online broker included. Merge-consistency filter - --min-image-cc gated on a per-image CC computed BEFORE the stills partiality post-refinement and never refreshed; the refiner now recomputes it, so the reported CC describes the data that are actually merged. - Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the merge, the error model and MergeStats can no longer disagree about which images are in (the --scale path merged unfiltered while its statistics were filtered). Per-image B-factor refinement (-B) removed - Measured on four serial-stills datasets: it is a no-op where the per-image fit is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on 14-25% of images). It had also been silently DISCARDED since the partiality post-refinement landed - reported but not applied. Rather than fix and keep a knob with no demonstrated benefit, the flag and the whole image_scale_b_factor chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs. ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS. (The Wilson per-image b_factor is a different quantity and stays.) Stills partiality width now fits both of its components - sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d* with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2 on d*^2. The angular-only width is fitted over a d*^2-dense population, so it was pinned by the high-resolution edge and collapsed at low d*: median partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55% of them under the merge's partiality floor, and the survivors divided by those values - which inflated the merged low-resolution intensity scale 3.6x (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x, no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining R-free are all blind to that ramp, which is why it survived earlier validation; the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged). Removed dead code from add-then-remove churn - Prediction-time "still partiality" (unreachable: no setter), the phantom IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the constant it always was), StillsPartialityRefine's caller-less Settings constructor and its reference to a long-gone env var, ProcessImage's unread bool return, an unused include, and a dead viewer overlay hook. Also - Viewer: the magnifier compared a QImage with itself, so its scene rect was set once ever and it could not pan into a larger dataset; the hover tail timer could fire after leaveEvent and resurrect the resolution readout outside the image. - update_version.sh regenerated the frontend lock file BEFORE bumping the version (every release shipped an off-by-one lock), and did git rm/git add on a path that has not existed since the client moved to src/client - with no set -e, both failed silently. - fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a redirect, not a test, so dkms add never ran. - Unit tests for the adaptive-threshold host functions, which had none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-27 09:07:00 +02:00
leonarski_fandClaude Opus 5	38f1c1a387	Revert "Viewer: read the data-analysis algorithm documentation from Help" ... This reverts commit 681e80e46. Dropped for now: QTextBrowser::setMarkdown leaves the inline LaTeX in CPU_DATA_ANALYSIS.md as raw "$...$" source, and the document's own HTML/math rendering wants sorting out first. Reverted rather than rewritten so the implementation stays available in history to bring back afterwards. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 22:08:45 +02:00
leonarski_fandClaude Opus 5	6f15ae04b7	Viewer: read the data-analysis algorithm documentation from Help ... Adds Help > Data Analysis Algorithms, showing docs/CPU_DATA_ANALYSIS.md in a window. The document is baked into the binary through the Qt resource system (aliased to :/cpu_data_analysis.md), so it needs no docs/ directory at runtime and cannot drift from the build it shipped with. Same shape as the existing third-party licences window, created once and raised thereafter. Limitation worth knowing: QTextBrowser::setMarkdown renders the headings, lists, emphasis and inline code well, but it has no math support, so the inline LaTeX in the more quantitative sections appears as raw "$...$" source. The descriptive material - which is most of the 744 lines - reads fine. Fixing that properly means either pre-rendering the document to HTML with a math filter at build time, or sending the user to the Read The Docs copy instead; neither seemed worth doing without knowing which you would prefer. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 22:05:11 +02:00
leonarski_fandClaude Opus 5	79b86164a4	Viewer: ROI statistics appear as soon as the first ROI is drawn ... Drawing an ROI reported Sum 0 and Max 0 until the next frame was loaded, with only the pixel count looking right because that comes from the ROI map rather than from the data. SetROIDefinition_i called RunROIOnly, which integrates whatever the preprocessor buffer already holds. LoadImage_i only preprocesses an image when a ROI is already defined, so the very first ROI is drawn on an image that was never preprocessed: the buffer is empty and every sum integrates to zero. From the next frame on a ROI exists, LoadImage_i preprocesses, and the numbers look correct -- which is what made this look like a refresh problem rather than a wrong call. Use AnalyzeROIOnly, which preprocesses the image before integrating. It costs a pass over the image per ROI edit, of the same order as one recolour, and ROI edits already keep at most one recompute in flight (live_pending_ in JFJochDiffractionImage), so the editing rate is bounded. I did not measure the drag rate specifically. Verified with a single frame loaded and no frame step: the first ROI drawn over the beam centre reports Sum 66065, Max 2761, Mean 0.473, centre of mass (787.3, 844.5). The Max equals the image's own reported maximum of 2761, as it must for a box containing the brightest pixel. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:49:02 +02:00
leonarski_fandClaude Opus 5	84a1538495	Viewer: drop the in-view ROI accumulation, the worker already does it ... The statistics shown for a drawn ROI do not come from the view at all. Drawing one promotes it to a named ROI, roiGeometryEdited goes to the reading worker, and the worker's per-image results arrive in ImageData().roi, which is what the Inspector's ROI section displays. So accumulateROI/CalcROI/roiCalculated were a second implementation of the same thing whose output nothing read -- and the worker's version is the better one: it handles the mask and it persists per image. Remove them. The view now owns only the ROI's geometry and gestures, which is all the worker needs from it. This corrects the previous commit's claim that nothing surfaces ROI statistics: the Inspector does, via the worker. Verified by drawing a box over the beam centre: Sum 65453, Max 1634, Mean 0.468, centre of mass (786.3, 843.4) against a beam centre of (764, 850). Note the numbers appear from the next analysed frame onward, since the worker attaches them at analysis time and the displayed frame was analysed before the ROI existed -- that behaviour is unchanged here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:42:30 +02:00
leonarski_fandClaude Opus 5	57f9e42382	Viewer: the region of interest belongs to the diffraction view alone ... Drawing an ROI only means something where there are detector counts to accumulate. Gate the gesture on a virtual AllowROI(), true only for JFJochDiffractionImage: shift-drag, the resize handles, the hover cursor and the "Clear ROI" context entry now do nothing in the azimuthal, grid-scan and calibration views, which cannot report anything about a box anyway. The statistics move out of the base class into the diffraction view and read the int32 image directly, so no float copy of the detector image is built for them either. With the labels already converted, image_fp is now untouched by the diffraction view, and the lazy EnsurePixelValues machinery it needed is gone. image_fp stays as the base's representation for the views whose data really is float: the azimuthal profile, the grid-scan 1/sigma^2 map, and the calibration viewer's eight source types. Removed with it: the ROI readouts in the calibration and 2D azimuthal windows, which were the only two consumers of roiCalculated -- the diffraction view emitted it and nothing listened. Nothing surfaces ROI statistics now; the pixel-mask case wants rectangles counting excluded pixels and deserves its own design. JFJochViewerROIResult is still used by the side-panel ROI list, so the widget stays. Verified in the GUI: shift-drag in the diffraction view still draws the box, turns it into a named ROI and runs the statistics; fit-view panel remains pixel-identical to the pre-series baseline. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:32:47 +02:00
leonarski_fandClaude Opus 5	27615a8a1d	Viewer: label pixels from the int32 image, and paint them instead of building items ... Two changes to the per-pixel value labels, which appear above 30x zoom. They were up to 5000 QGraphicsSimpleTextItems created and destroyed on every overlay rebuild - so on every pan step while zoomed in. Paint them in drawForeground() instead: no item churn, no scene invalidation, and the text is laid out in viewport pixels so it is a constant readable size rather than a scene-space font scaled by 0.2. Same approach as the magnifier's labels. The value text becomes a virtual, PixelLabel(). The base still formats from image_fp, which is what the genuinely float-valued views hold (azimuthal profile, grid-scan 1/sigma^2, the calibration viewer's eight source types). JFJochDiffractionImage overrides it to read the int32 image directly: counts are exact integers, so routing them through float32 is a detour that also cannot represent summed values above 2^24 exactly. Verified at 38 wheel clicks over a module edge: identical values and gap/contrast handling to the previous float path, now centred in each pixel. Fit-view panel still pixel-identical to the pre-series baseline. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:27:17 +02:00
leonarski_fandClaude Opus 5	7a893bb1e7	Viewer: per-pixel counts in the magnifier, read from the int32 image ... Users expect a magnifier to tell them the counts, which the follower view could not do: it has the rendered pixels but not the numbers behind them. Take them from the detector's int32 buffer directly, the same source the main view colours from, so no float copy of the image is needed - the magnifier still holds nothing full-size of its own, only a shared_ptr to the frame and one to the reader image. The labels are painted in drawForeground() rather than as scene items. The main view creates up to 5000 QGraphicsSimpleTextItems per overlay rebuild for this; here they are just drawn, so there is no item churn and no scene invalidation. Text is laid out in viewport pixels so it stays a constant readable size, and black/white is chosen from the luminance of the rendered pixel underneath, as the main view does. Threshold is the same 30x as the main view, so the default 12x magnification shows no labels until the user wheels in; a cap keeps pathological window sizes from drawing thousands of them. Verified in the GUI at 32x: counts drawn per pixel with white text over the dark centre of a Bragg peak and black elsewhere, and "Gap" across a module gap. Main image panel still pixel-identical to the pre-series baseline. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:18:20 +02:00
leonarski_fandClaude Opus 5	d2ce65f857	Viewer: magnifier displays the frame the main view already rendered ... The magnifier and the main view are two views of the same image at different position and zoom, but the magnifier ran the whole pipeline again on its own copy: it wrapped the same int32 buffer in a SimpleImage, converted it to float, coloured every pixel and kept its own full-size QImage. That is a second conversion and two extra full-detector buffers (20 MB at 2.8 Mpx, 138 MB at 18 Mpx) to feed a 320x320 window. Separate producing a frame from displaying one: - JFJochImage keeps the rendered frame in a shared_ptr<QImage> (the pointer is stable for the widget's lifetime; only the contents change, so the existing buffer reuse is unaffected), publishes it via Frame() and announces new pixels with frameRendered(). - JFJochImageItem holds that shared_ptr instead of a reference to a member of its owner, which also removes a lifetime coupling. - JFJochFollowerImage is a small read-only view of such a frame with its own zoom and centre. It shows only the image: overlays, ROI tools and per-pixel labels belong to the view that owns the data. - The magnifier becomes one of those, fed from frameRendered(). Consequences beyond the saving: the magnifier now agrees with the main view on colour map, contrast and HDR mode, which it never did -- it was wired to neither, so it always drew with its own defaults. And the visibility guard added in 6d1af4921 is gone: there is no longer any per-frame work to skip, so nothing needs guarding. That guard was a workaround for this design. Stepping 30 frames with the magnifier open: 5550 -> 4810 ms CPU, which is what it costs with the magnifier closed (4770 ms) -- it is now free either way. Verified: main image panel and a drag-pan stay pixel-identical to the pre-refactor binary (AE=0); the magnifier follows the cursor, updates on a new frame, and now tracks a colour-map change. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:11:42 +02:00
leonarski_fandClaude Opus 5	5782cc0edf	Viewer: reciprocal-space view does nothing while its window is closed ... The window is a placeholder for future functionality and is closed almost all of the time, but it extracted the frame's spots and rebuilt and uploaded its vertex arrays on every image, whether or not anything was on screen. Guard it in rebuildGL() rather than at each of the eight call sites, so any future caller inherits the behaviour: while hidden it only records that a rebuild is owed, and showEvent() pays it. imageLoaded() additionally skips extracting the frame's spots, which is the other half of the per-frame work. The OpenGL code path is untouched and still built and exercised the moment the window is opened. Note: I could not show a CPU saving for this on the headless test machine -- there, ~74% of the process CPU is Mesa llvmpipe software rasterisation that I was unable to attribute to any per-frame code path, and it swamps the effect. The work being skipped is nonetheless unambiguously unnecessary. Verified in the GUI: after stepping frames with the window closed, opening it shows the current frame's spots, and it keeps updating while open. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 21:05:21 +02:00
leonarski_fandClaude Opus 5	68f5f1f32d	Viewer: do not render the magnifier close-up while it is closed ... centerAt() checked isVisible(), but imageLoaded() did not, so every frame built a SimpleImage over the whole detector image and ran it through the full JFJochSimpleImage path -- convert to float, colour every pixel, redraw -- to feed a 320x320 window that is closed by default and stays closed most of the time. Remember the frame instead and do the work in showEvent(). Holding the shared_ptr also keeps alive the buffer that the SimpleImage's CompressedImage points into, which it did not own. Stepping 30 frames with the magnifier closed: 5545 -> 4770 ms CPU (-14%), on a 2.8 Mpx detector; the saving is per-pixel, so it grows with detector size. With the magnifier open the cost is unchanged (5500 ms), which is what was being paid unconditionally before. Verified in the GUI: opening the magnifier still populates it, and it still refreshes when the frame changes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 20:45:11 +02:00
leonarski_fandClaude Opus 5	2a31cf8d81	Viewer: stop forcing FullViewportUpdate in JFJochSimpleImage ... FullViewportUpdate redraws the whole viewport on any change. The attached comment ("keep overlays in pixel units independent of zoom") does not describe what the setting does, and nothing here needs it: SmartViewportUpdate repaints the changed rectangles and falls back to a full repaint by itself once there are too many to be worth tracking. This is the view used by the calibration window and the magnifier, and the magnifier is driven from every hover, so on a remote session it repainted its whole viewport per pointer motion. Note: not exercised visually -- both windows are opened from menus, which the headless harness does not drive. The change is a repaint-mode switch with no effect on what is drawn. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 20:13:21 +02:00
leonarski_fandClaude Opus 5	4892c57119	Viewer: paint the resolution readout in drawForeground, not as a scene item ... The hovered "d = ... A" readout was a QGraphicsTextItem flagged ItemIgnoresTransformations, repositioned on every mouse motion. Qt cannot compute a tight dirty rect for an item that ignores the view transform, so it marks the entire viewport dirty whenever such an item moves or changes text -- and this one moved constantly. Paint it in drawForeground() in viewport pixels instead, and repaint only the union of its old and new rectangles. That also removes the item lifetime special-casing: it was deliberately kept out of overlay_items_, had to be nulled by hand after scene()->clear(), and carried comments in three places warning about the dangling pointer. This does not reduce raw X11 traffic -- there every repaint uploads the whole window whatever the damage -- but it cuts the work per hover, and it does matter under a compressing remote protocol (VNC/NX/xpra), which encodes only the region that actually changed. Verified against the previous build: same text, colour and position. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 20:13:04 +02:00
leonarski_fandClaude Opus 5	501ce1ba3d	Viewer: rate-limit hover feedback to ~15 Hz ... The status bar, the resolution readout and the magnifier were all regenerated on every single mouse motion event. Each regeneration repaints, and on a remote X session a repaint uploads the whole window regardless of how little changed, so the pointer merely crossing the image saturates the link: measured with a counting relay in front of the X server, 50 motions over the image cost 273 MB, and a build with the hover work removed cost 18 KB. Rate-limit it. Two details matter: - The limit is applied inline, not from a timer. Running the update inside the mouse event keeps its damage in the same repaint as anything else that event triggers (a pan). A first attempt deferred the work to a timer instead, which split one repaint into two and made panning measurably worse. - The catch-up that reports the final position is debounced, not queued per skipped motion, so it fires once after the pointer stops rather than repeatedly mid-gesture. mouseHover() now takes the scene position and modifiers instead of the event, which also removes the identical mapToScene() from all four implementations. Hover traffic over 3 repeats: 173 MB mean -> 140 MB, and the run-to-run spread drops from +-14% to +-2%. The harness tops out near 30 motions/s, barely above the 15 Hz limit; a real mouse reports far faster, where the cap does more. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 20:12:36 +02:00
leonarski_fandClaude Opus 5	3eccc58961	Viewer: colour the diffraction image straight from int32 ... image_fp is the base class's one pixel representation, and it earns that for three of the four image widgets: the azimuthal image is already float, the grid scan holds computed 1/sigma^2 floats, and the calibration viewer accepts eight source types from uint8 to float64. The diffraction image is the odd one out -- its source is a large int32 buffer -- and it is the one paying: a full int32 -> float pass plus a second resident copy of the image, on every frame. Split the mapping from the source. PixelColorMap holds the precomputed LUT constants and does value -> colour; a virtual ColorRow() picks the pixels out of whatever buffer the subclass has. Both paths now go through the same Apply(), so only the gap/bad/saturated dispatch differs, and it lines up exactly with the encoding LoadImageInternal used: GAP_PXL_VALUE -> NAN -> gap ERROR_PXL_VALUE -> -INF -> bad SATURATED_PXL_VALUE -> +INF -> saturated The base class still needs real pixel values for ROI statistics and per-pixel labels, so image_fp is filled on demand instead of per frame -- and only when something reads it: a non-empty scratch ROI, or labels above 30x zoom. Neither happens while simply looking at frames, and nothing else routinely sets roiBox (the named ROIs are computed in the reading worker, not here). 18.1 Mpx: 10.5 -> 5.9 ms per frame and 72 MB less resident. 4.5 Mpx: 1.8 -> 1.0 ms and 18 MB. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 19:12:55 +02:00
leonarski_fandClaude Opus 5	0b926af5af	Viewer: cache the traced resolution-ring contours ... DrawResolutionRings traced every ring point by point on each overlay rebuild: 361 ResPhiToPxl calls per ring, so about 4000 geometry evaluations per rebuild with the 11 ice rings shown -- and a rebuild happens on every pan step. The contours depend only on the ring list and the geometry, neither of which changes while the view moves, so keep them. The cache is keyed on the ring list (which RingMode::Auto recomputes from the visible area, so it still re-traces when it should) and cleared in loadImage for a possibly-new geometry. Labels are still placed per rebuild: they depend on the visible rect. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 19:04:52 +02:00
leonarski_fandClaude Opus 5	c3eba650e9	Viewer: one overlay rebuild per pan/zoom, and only invalidate the image when it changed ... Panning called updateOverlay() three times per mouse move: once for each scrollbar's valueChanged -> onScroll(), then once explicitly. Zooming was the same. Every one of those tore down and rebuilt every overlay item. Suppress onScroll() for the duration of the gesture instead, and let the gesture do its single rebuild at the end. Note this cannot be done by blocking the scrollbars' signals: QAbstractScrollArea drives the actual scrolling off valueChanged, so blocking it would stop the view moving at all. updateOverlay() also refreshed the image item unconditionally, which marks the whole item dirty and forces a full-viewport repaint even though pan and zoom never change the pixels. Track whether RenderImage has run since the last refresh and skip it otherwise. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 19:03:05 +02:00
leonarski_fandClaude Opus 5	fd9f93e1f1	Viewer: stop copying the image in LoadImageInternal, parallelise it ... "auto img = image->Image()" deduced std::vector<int32_t> by value, so every frame copied the whole detector image before converting it -- 72 MB on a 16 Mpx detector. Bind a const reference instead. The sentinel-to-float conversion also ran single-threaded on the GUI thread; spread it over rows the same way RenderImage does. 18.1 Mpx: 11.8 -> ~1 ms, plus the copy that is now gone. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 19:00:37 +02:00
leonarski_fandClaude Opus 5	417170bc13	Viewer: coalesce foreground/background recolours ... Ctrl+wheel, Shift+wheel and the foreground slider each recoloured the whole image synchronously, once per input event. On a large detector the recolour is slower than the events arrive, so they queued up and the view lagged behind the cursor for as long as the user kept scrolling. Defer the recolour to a zero-delay single shot and drop the intermediate values: at most one recolour is in flight, and it always uses the newest foreground/background. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 18:59:45 +02:00
leonarski_fandClaude Opus 5	a704a2cd33	Viewer: draw the rendered image directly instead of via a QPixmap ... Every recolour ended with QPixmap::fromImage(), which allocates a second full-size buffer and converts the whole image into the screen format. That conversion was the largest single cost left in the colouring path. Replace QGraphicsPixmapItem with a small item that paints qimg_buffer_ with QPainter::drawImage. The buffer is already what the raster engine wants, so nothing is converted or copied. The item declares its opaque area, as the pixmap item did, so the view still skips the background fill underneath it, and it turns SmoothPixmapTransform off before drawing to keep the nearest-neighbour sampling QGraphicsPixmapItem gave us by default -- zoomed-in detector pixels stay sharp squares. GeneratePixmap is renamed RenderImage: it no longer makes a pixmap. 18.1 Mpx recolour: 22 -> 5.6 ms (28.0 ms before this series). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 18:58:55 +02:00
leonarski_fandClaude Opus 5	0cee55f654	Viewer: drop the full-size image_rgb mirror ... GeneratePixmap wrote every pixel twice: once into the QImage and once into image_rgb. The only reader was writePixelLabels, which needs a colour for at most 5000 pixels and only above 30x zoom, so the mirror cost a W*H*3 buffer and a second store per pixel to serve a fraction of a percent of them. Read the colour back from the rendered image instead. 18.1 Mpx colouring loop: 9.5 -> 6.2 ms. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 18:56:17 +02:00
leonarski_fandClaude Opus 5	96e10fd1f0	Viewer: reuse the QImage buffer in GeneratePixmap ... The qimg_buffer_ member was added to avoid reallocating the full-size image every recolour, but GeneratePixmap still built a local QImage and the member was never referenced. Wire it up: the buffer is reallocated only when the image dimensions change. The data pointer is taken once, before the parallel loop. scanLine() is non-const and would otherwise have every worker detach the buffer at the same time, which is a data race as soon as the buffer is shared with the pixmap. 18.1 Mpx recolour: 28.0 -> 22 ms (measured on the colouring path alone). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-26 18:55:22 +02:00
leonarski_fandClaude Opus 4.8	a8c1006c49	Choose min-pix-per-spot adaptively per image for serial-stills indexing ... For stills indexing the minimum-pixels-per-spot filter is now chosen per image instead of being fixed: the frame is indexed at min-pix 3/2/1 and the setting that maximises indexed-spot count weighted by indexed fraction (n_indexed^2 / n_total) is kept, then integrated once at that min-pix. The fraction factor keeps a smaller min-pix's extra spots only when the lattice actually explains them, so strong frames retain their real weak spots (extending resolution) while noise-flooded frames stay strict. The mode is selected by the presence of --min-pix-per-spot, now optional (SpotFindingSettings::min_pix_per_spot is std::optional<int64_t>): omit it for the adaptive per-image path, give a value to force a fixed min-pix. It applies only to the stills indexing path -- rotation indexing builds one global lattice and keeps a fixed min-pix, and the online receiver and the FPGA host path always carry a concrete value, so neither changes. IndexAndRefine::ProcessImage now returns whether the frame indexed, to drive the per-image selection. Exposed in the jfjoch_viewer spot-finding settings (adaptive-threshold and adaptive-min-pix checkboxes, each greying out the control it overrides); the broker uses neither. Validated on the full rotation regression battery (no regression) and the whole serial-stills target battery at full image count. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-26 18:31:35 +02:00
leonarski_fandClaude Opus 4.8	9fdeed282a	Add fused GPU adaptive spot finder (azint + spot finding in one pass) ... AdaptiveSpotFinderGPU does the per-resolution-ring reduction once on the GPU and drives both products from it: the azimuthal-integration profile (corrected space) and the self-calibrating adaptive spot-detection threshold (raw counts). This replaces the separate GPU azint pass and the host-side adaptive spot finder that runs on the GPU path today. On a ~4.5 MP detector it does both jobs in ~1 ms/frame versus ~40 ms for the CPU adaptive finder (~42x), with an identical spot list and azimuthal profile. The per-ring threshold math (Poisson tail + read-floored Gaussian, operating point from the false-pixels-per-frame knob) is factored into AdaptiveThreshold.h so the CPU and GPU finders share one source of truth and cannot drift. Wired opt-in via a MXAnalysisWithoutFPGA constructor flag, default on for the rugnux offline path and the interactive viewer, off for the online receiver (so the broker path is unchanged). When on, Analyze() skips the separate azint pass and lifts the profile from the fused engine. The viewer gains an "Adaptive threshold" checkbox that greys out the signal/noise and photon-count sliders (the adaptive finder uses neither). Dedicated tests exercise both products (spot-finding parity vs the CPU finder, azimuthal profile vs a standalone GPU azint) plus a speed benchmark. Validated end-to-end on lysozyme serial stills: fused == CPU-adaptive index rate and merge stats. Docs: new section 3.2 in docs/CPU_DATA_ANALYSIS.md. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-25 20:10:45 +02:00
leonarski_fandClaude Opus 4.8	014e43a4c9	Remove non-helping stills merge/scaling knobs ... Trims three opt-in stills parameters that did not improve data quality on the external-reference (PDB R-free) battery and only added code: - --partiality-uncertainty: the (1-p)/p merge-sigma term was null on all four serial-stills datasets of the battery vs their reference structures (and neutral-to-harmful at higher coefficients); removed the flag, setting and CorrectedSigma term. - --stills-modulation: the detector-plane flat-field surface was net-negative on flooded data; removed the flag, setting and MergeOnTheFly::RefineModulation (the rotation modulation in RotationScaleMerge is unaffected). - --min-indexed-fraction: every value other than the 0.20 default collapsed CC1/2; removed the override flag/setter, keeping the fixed 0.20 acceptance floor. Default behaviour is unchanged (all three were off / at their default). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-25 17:40:48 +02:00
leonarski_fandClaude Opus 4.8	1a2b0181a5	Add physical partiality post-refinement for stills (default on) ... Replace the frozen scalar-sigma stills partiality with a physical, refined model. Per crystal, refine an orientation tilt (dpsi_x, dpsi_y) against the running merge and recompute each reflection's partiality analytically from the refined geometry (angular Ewald-proximity model, sigma(d*) = gamma_e*d*), with the per-crystal scale G profiled out by the existing robust IRLS - no re-integration. A soft Gaussian prior on dpsi tames weak-data overfit while staying inert on strong data. The merge <-> refine loop iterates a few times. This is now the stills default via ScalingSettings::stills_partiality_refine (on). A single opt-out flag `--simple-stills` reverts to treating every reflection as a full (p=1, single pass). Retires the experimental `--still-partiality` flag. The viewer gains a "Partiality post-refinement (stills)" checkbox in Scaling settings. Validated (integrate-once / --scale): CC1/2 and R_meas both improve on three monochromatic serial-stills datasets (+2.8 / -10, +5.6 / -3.4, +2.1 / -4); neutral on a pink-beam DMM set (already-full reflections); R-free/R-work down vs a fixed model; competitive with CrystFEL partialator on matched frames. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-23 14:45:43 +02:00
leonarski_f	67dca388bd	v1.0.0-rc.160 (#70) ... 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: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-19 09:39:28 +02:00
leonarski_f	451310f43d	v1.0.0-rc.158 (#68) ... 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. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-12 19:42:29 +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	54c667190f	v1.0.0-rc.155 (#65) ... 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: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +02:00
leonarski_f	c49bd2ac3b	v1.0.0-rc.152 (#62) ... * 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	2026-06-17 20:36:24 +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	75de40f52b	v1.0.0-rc.147 (#57) ... 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>	2026-06-02 11:49:24 +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	d760b12a18	v1.0.0-rc.141 (#51) ... 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: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times * frontend: Fix selection of FFTW in indexing settings Reviewed-on: #51 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 13:04:54 +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	c981e1b91c	v1.0.0-rc.137 (#46) ... 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	2026-04-25 19:59:21 +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	6133da1377	v1.0.0-rc.133 ... 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: Use httplib for HTTP server instead of Pistache * jfjoch_broker: Drop OpenSSL support * jfjoch_broker: Base work for multi-lattice support in the future * Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib) Reviewed-on: #41	2026-03-26 20:50:33 +01:00
leonarski_f	f3e0a15d26	v1.0.0-rc.127 (#34) ... 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.124. * jfjoch_broker: Default EIGER readout time is 20 microseconds * jfjoch_broker: Multiple improvements regarding performance * jfjoch_broker: Image buffer allows to track frames in preparation and sending * jfjoch_broker: Dedicated thread for ZeroMQ transmission to better utilize the image buffer * jfjoch_broker: Experimental implementation of transmission with raw TCP/IP sockets * jfjoch_writer: Fixes regarding properly closing files in long data collections * jfjoch_process: Scale & merge has been significantly improved, but it is not yet integrated into mainstream code Reviewed-on: #34	2026-03-02 15:57:12 +01:00
leonarski_f	1ab257af6c	v1.0.0-rc.125 (#32) ... 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>	2026-02-18 16:17:21 +01:00
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	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	b02c412d59	v1.0.0-rc.118 (#25) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_viewer: Fix issue when HTTP sync silently disconnected when it was enabled when the broker was starting measurement. * jfjoch_broker: Add protections on time of geometry optimization and reduce rotation recalculations Reviewed-on: #25 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-06 20:05:30 +01:00
leonarski_f	d1a4c19ef3	v1.0.0-rc.117 (#24) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_viewer: Add ROI results to the dataset info plots * jfjoch_writer: Remove HTTP interface, as it is not needed/used at the moment Reviewed-on: #24 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-05 22:03:07 +01:00