Removes azim_int_settings.sigma_clip / rugnux --azim-sigma-clip and the clipping
machinery in AzIntEngine. This is a partial revert of a6be35ccd - the ice-ring-mask
removal that commit also carried stays. Sigma clipping remains where it started and
where it is needed: inside the adaptive spot finder, at a fixed 3 sigma on raw
counts, feeding the detection threshold and the ice score.
The option made the workflow harder to reason about than the quantity was worth. It
gave azimuthal integration two meanings behind one setting - the bin mean and the
background under the peaks - which the azimuthal-integration workflows do not need.
It also did not compose with the fused GPU engine, which supplies the profile from
its PLAIN pass: on the default rugnux, viewer and receiver path the setting was
silently doing nothing (measured, the profile came out identical to the unclipped
run to 1e-6 with identical per-bin pixel counts). Making it correct is not a matter
of gating that one shortcut - it means separating the workflows (azimuthal
integration, MX rotation, MX stills, geometry calibration) and deciding per workflow
what the profile is for, which is a larger change than the option earns.
The default path is unaffected: over 20 images of a rotation dataset the radial
profile, the per-bin pixel counts and the spot counts are unchanged.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The profile is the MEAN of each bin, so a few strong reflections landing in a bin
lift it exactly as a smooth powder ring does. That is the wrong quantity whenever
the profile is wanted as a background rather than as a measurement of what is in
the bin - the ice score being the case in point, where reading a plain profile
INVERTED the metric: over 37 rotation crystals the two highest-scoring crystals
had no ice at all.
The adaptive spot finder already computes the right thing, a sigma-clipped
per-resolution-ring background, as a byproduct of its own threshold. Where it
runs, the ice score uses that. Where it does not - --no-adaptive-spots,
--azint-only, and anything reading the profile the broker wrote - there was no way
to get it. This adds one: azim_int_settings.sigma_clip (rugnux --azim-sigma-clip),
0 = off, minimum 2 because a tighter clip rejects a large part of a clean Gaussian
bin and biases the estimate low rather than removing outliers.
Two clip passes follow the plain one, matching the finder's recipe - the first
pass's standard deviation is itself inflated by the peaks being removed, so one
pass leaves a threshold that is still too generous. A bin with fewer than eight
pixels is left alone: at the detector edge and behind the beam stop there is no
spread to clip on.
Both engines do it. On the GPU the accept range is computed by a small kernel and
stays resident, so a clip pass is one more read of the same pixels and no round
trip; the two accumulation kernels take the range as a pointer that is null on the
plain pass. Measured on a JUNGFRAU rotation dataset, non-adaptive path: azimuthal
integration 0.02 -> 0.06 ms per image, exactly the 3x the extra passes predict,
against a 0.34 ms per-image total.
Note what the result IS: the smooth background under the peaks, not the bin mean.
It should not be switched on where a ring's integrated intensity is wanted - the
powder-ring geometry fit reads ring peaks, and those are what a clip is designed
to remove. Off by default, so nothing changes unless it is asked for.
Not exposed over the REST API - that needs the generated model regenerated, which
is a separate step.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Making the high limit optional removed the implicit upper bound on the low one
(it used to follow from high <= maxQ and high > low), so --azim-min-q 50 with no
maximum is accepted and ResolveHighQ then calls std::clamp with its lower bound
above its upper bound, which is undefined.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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>
* jfjoch_broker: When in FPGA workflow (with PSI detectors) azimuthal integration might be forced to CPU - this will require more computational power, but it enables more integration bins and reports standard deviation of each bin.
* jfjoch_broker: Raise error if one is in FPGA flow and there are too many azimuthal integration bins.
Reviewed-on: #60
leonarski_fandClaude Opus 5