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>
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>
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
* 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
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 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>
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>
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
leonarski_fandClaude Opus 5