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>
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>
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: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start`
* jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start'
* jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time
* jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received
* jfjoch_broker: Use nanoseconds internally for frame/image/readout time
* jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished)
* jfojch_broker: Improve profiling of different data analysis steps
* jfjoch_broker: Record integration reflection count
* jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds)
* jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked
* jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets
**Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time.
Reviewed-on: #49
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: Better track time for each operation in the processing stack
* jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress)
* jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress)
* jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0)
Reviewed-on: #46
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: Use httplib for HTTP server instead of Pistache
* jfjoch_broker: Drop OpenSSL support
* jfjoch_broker: Base work for multi-lattice support in the future
* Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib)
Reviewed-on: #41
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: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files)
* jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction
* jfjoch_broker: Image pusher statistics are accessible via the REST interface
* jfjoch_writer: Supports TCP image socket and for these auto-forking option
Reviewed-on: #36
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release.
* jfjoch_broker: Add thresholding to prefer shorter vectors after FFT
* jfjoch_broker: Add experimental mosaicity estimation for rotation experiments (this is work in progress)
* jfjoch_viewer: Display file opening errors
* jfjoch_viewer: When loading files over DBus add retry/back-off till the file is available
Reviewed-on: #29
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release.
* jfjoch_viewer: Minor polishing of new functionality
* jfjoch_broker: User NaN for empty azimuthal bins
Reviewed-on: #12
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5