38 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	a95aca382c	Remove dead code left behind by recent changes ... None of this has a reader: - ScalingSettings::scaling_regularize and its setter/getter - ScaleOnTheFlyResult::succesful (never set) and ::time_s (set, never read), with the timing that only fed the latter - JFJochImage::last_fit_viewport_ (written twice, read nowhere) and the comment claiming the retry uses it - the retry keys off initial_fit_done_ - JFJochDiffractionImage::ice_ring_width_Q_recipA, and a QtConcurrent include in a file that uses none - an unused gemmi::Op accumulator in the spindle-angle helper - <random> in Merge.{h,cpp}, from before the half-set split became a hash - an orphaned comment describing the Ceres B-factor residual deleted in 014e43a4c, and two trailing comments that had collided on one line Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:29:42 +02:00
leonarski_fandClaude Opus 5	379feac2e9	Viewer: lay out pixel labels only for the area being repainted ... drawPixelLabels took its range from the whole viewport rather than from the exposed rect it was given, so a 200x40 px hover repaint still walked up to 5000 cells doing mapFromScene + QImage::pixel + drawText for each, only to have the result clipped away. With hover feedback now rate-limited to 15 Hz that ran ~75 times a second at high zoom, against once per overlay rebuild before the rendering rework. Intersect with the exposed rect; same in the magnifier. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:22:27 +02:00
leonarski_fandClaude Opus 5	dc5721ad8a	Viewer: repaint the resolution readout when the view scrolls ... The "d = ... A" readout moved from a scene item flagged ItemIgnoresTransformations to a fixed viewport position painted in drawForeground, which is what made a hover update dirty a small rect instead of the whole viewport. But QGraphicsView pans by blitting the viewport: the painted text is shifted along with the image and left there, and the pending update for its old position is translated away too, so dragging the image smears ghost copies of the readout across the corner. Dirty the old and the new rect when the view scrolls - still a couple of hundred pixels, not the viewport. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-30 11:22:27 +02:00
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	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	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_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	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	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	cc3eb8352c	v1.0.0-rc.148 (#58) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_broker: Improve azimuthal integration (add <I^2> calculation) * jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated) * jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin Reviewed-on: #58	2026-06-08 08:30:35 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00
leonarski_f	bb9f5c715f	v1.0.0-rc.135 (#44) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-16 11:59:59 +02:00
leonarski_f	07fe4dd3bb	v1.0.0-rc.124 (#31) ... This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. * jfjoch_broker: Improve refection position prediction and Bragg integration code. * jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. * jfjoch_writer: Fix saving mosaicity properly in HDF5 file. * jfjoch_viewer: Introduce high-dynamic range mode for images * jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) * jfjoch_viewer: Zoom-in numbers have better readability Reviewed-on: #31 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-01 13:29:33 +01:00
leonarski_f	1c4dfd03e2	v1.0.0-rc.123 (#30) ... This is an UNSTABLE release. * jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility * jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) * jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) * jfjoch_viewer: Add more color schemes for better image readability * HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable * HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists Reviewed-on: #30 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-01-30 13:43:09 +01:00
leonarski_f	e2b240356c	v1.0.0-rc.121 (#28) ... This is an UNSTABLE release. * jfjoch_broker: Report changes in the image buffer, so viewer doesn't reload constantly * jfjoch_viewer: Improve performance of loading images * jfjoch_viewer: Auto-throttle image loading in HTTP-sync / movie modes * jfjoch_viewer: Auto-foreground calculated with histogram * jfjoch_viewer: Fix rare segmentation fault Reviewed-on: #28 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-12 21:24:20 +01:00
leonarski_f	36d0507758	v1.0.0-rc.119 (#26) ... This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). * jfjoch_broker: Add binary export of data analysis plots over OpenAPI * jfjoch_broker: Minor fixes to HTTP error handling * jfjoch_viewer: Prefer binary plots over JSON plots * jfjoch_viewer: Change foreground with F button + wheel * jfjoch_viewer: Change way how angles are displayed * jfjoch_viewer: Display resolution of the mouse cursor in top left corner Reviewed-on: #26 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-12-08 19:53:35 +01:00
leonarski_f	9bc71cfddc	v1.0.0-rc.111 (#17) ... This is an UNSTABLE release. * jfjoch_viewer: Remove 3D lattice viewer (not really useful at this moment) * jfjoch_viewer: Fix auto contrast not refreshing image Reviewed-on: #17 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-28 16:22:18 +01:00
leonarski_f	224cc8b89c	v1.0.0-rc.110 (#16) ... This is an UNSTABLE release. * jfjoch_broker: Add auto-contrast option for preview images * Frontend: Add logo image * jfjoch_viewer: Add logo image * jfjoch_viewer: For image chart allow to set min value to zero * jfjoch_viewer: For resolution estimation plots, visualization uses 1/d^2 as measure * jfjoch_viewer: Add 3D unit cell visualization (experimental/WIP/not really there) * Documentation: Add logo image Reviewed-on: #16 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-28 12:47:35 +01:00
leonarski_f	05410d7cb3	v1.0.0-rc.109 (#15) ... This is an UNSTABLE release. * jfjoch_viewer: Add keyboard shortcuts and option to copy image to clipboard * jfjoch_broker: Fix bit-width and exposure time for PSI EIGER detectors Reviewed-on: #15 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-26 13:48:59 +01:00
leonarski_f	d53e93023b	v1.0.0-rc.108 (#13) ... This is an UNSTABLE release. * jfjoch_viewer: Fix bug when resolution estimation/B-Factor/Profile radius were not set (NaN) * jfjoch_viewer: Show spots is off by default, resolution ring mode is enabled by default * jfjoch_viewer: Fit to window of image is now default when size of the grid changes Reviewed-on: #13 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-24 12:27:54 +01:00
leonarski_f	ddcc24fba8	v1.0.0-rc.106 (#11) ... This is an UNSTABLE release. * jfjoch_viewer: Allow for multiple dataset info plots * jfjoch_viewer: Highlight current element in grid Reviewed-on: #11 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-21 11:03:29 +01:00
leonarski_f	a6b5cb5629	v1.0.0-rc.105 (#10) ... This is an UNSTABLE release. * jfjoch_viewer: Clean-up widgets slightly * jfjoch_viewer: Limit right panel to 600 pixels * jfjoch_viewer: Parse crystal symmetry type * jfjoch_viewer: Grid scan view takes color map and can be fit to zoom Reviewed-on: #10 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-20 09:46:25 +01:00
leonarski_f	95acf3aba3	v1.0.0-rc.104 (#9) ... This is an UNSTABLE release. jfjoch_writer: Fix and improve the way grid scan geometry is saved (non-NXmx extension makes it way easier) jfjoch_viewer: Display grid scan results in 2D (work in progress) jfjoch_viewer: Improve auto-scaling on start of images (work in progress) jfjoch_viewer: Add B-factor and resolution estimate to the dataset info plots Reviewed-on: #9 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-19 17:28:10 +01:00