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Commits
| Author | SHA1 | Message | Date | |
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  leonarski_fandClaude Opus 5
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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> |
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leonarski_fandClaude Opus 5
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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> |
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leonarski_fandClaude Opus 5
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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
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