Three independent changes to the CPU-bound parts of an offline rotation run, none
of which alters a result.
Candidate-cell refinement now splits across threads. RefineCandidateCells already
took a (block, nblocks) partition, but the only call site passed nblocks=1, so the
whole first pass of a two-pass rotation run sat on one thread per scheme - two
threads, unchanged at every -N, for a third of the run. A block touches only its
own scores(j) and cells rows and holds its own scratch, so the split is exact.
The budget is a new IndexingSettings::RefineThreads, left at 1 by default and set
only where few indexer threads exist: raising it unconditionally would
oversubscribe the paths that already run one indexer per image across all workers.
The mmCIF writer built a std::ostringstream per formatted number, twelve per
reflection. snprintf gives the same digits for 0.535 -> 0.220 s per file.
The space-group search built the same orbit mapping twice per candidate point
group - once for the merge chi^2 and once for the systematic-error b, an
apply_to_hkl and Canonicalize per observation per operator each time. Build it
once and hand it to both.
18 Mpx rotation set 24.6 -> 18.7 s, 2.5 Mpx 13.0 -> 10.7 s, and the 37-crystal
battery 13m55s -> 10m47s with no failures, the same 34/37 space groups, and
statistics unchanged on 30 of 37 (the rest drift within the run-to-run spread the
binary already had, which a control build with the split disabled reproduces).
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>
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>
Two opt-in tools for weak serial-stills tuning; both default-off, so the
default pipeline is bit-identical (verified: a serial-stills reference run
reproduces HEAD's 7.85% indexing rate exactly).
--local-snr <sigma> (AdaptiveSpotFinderCPU::FilterByLocalSNR): after the loose
per-ring adaptive threshold builds connected-component spots, drop any spot that
does not stand this many sigmas above its OWN LOCAL background (robust median/MAD
of a square annulus), not just the azimuthal ring mean. On structured-background
(XFEL) frames the ring mean underestimates the local diffuse level in some
sectors, so the ring threshold floods; a real Bragg peak still stands many local
sigmas proud. Validated on XFEL stills to separate real peaks from flood at the
pixel level (real median local-SNR ~70 vs flood ~2.6; SNR>=5 keeps ~99.8% of
real peaks, ~14% of flood). GPU-portable (a per-spot local reduction). NOTE: on
the current serial-stills battery it is index-rate/CC1/2 neutral -- the flood that
survives as CC clusters overlaps weak-real spots, and only lattice-fit separates
those -- but it is the correct tool for genuinely floody data (ice/jet/loosened
detector) and the right substrate for the online FPGA path.
--min-indexed-fraction <f>: exposes the previously hardcoded 0.20 minimum
indexed-spot fraction (AnalyzeIndexing) as a per-run setting. Lowering it admits
weaker/sparser crystals; on flooded XFEL data the extra lattices are spurious
(pair with --min-image-cc to gate them), on clean synchrotron data there are no
marginal frames so it is a no-op -- useful as a gating-experiment primitive.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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
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
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: Improve logic regarding indexing architecture and thread pools (work in progress).
Reviewed-on: #45
This is an UNSTABLE release and not recommended for production use (please use rc.11 instead).
* jfjoch_broker: Experimental rotation (3D) indexing
* jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values
Reviewed-on: #18
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5