Background estimate: use the mean of the local ring, not the median. For a
right-skewed (Poisson) background the median sits below the mean, so subtracting
it under-subtracts and biases every weak intensity positive; over multiplicity
this becomes fake <I/sig> of a few in no-signal high-resolution shells. Fixed in
both PixelRefine and BraggIntegrate2D (the classical route had the same bug).
<I/sig> now tracks CC honestly and the true resolution limit is visible.
Error model: fit a global a, b (XDS form sigma'^2 = a*sigma^2 + (b*I)^2) from the
scatter of symmetry equivalents at the merge level (so both integrators benefit),
and print it with ISa = 1/b in jfjoch_process. The (b*I)^2 term uses the
reflection mean (not the per-observation I_i, which biases the weights and
collapses CC); a,b come from a relative-weighted bin regression. Replaces the
earlier per-resolution-shell variant, which was partly masking the background bias.
METHODS.md: document both (Sections 6-7), integrator-agnostic.
Co-Authored-By: Claude Opus 4.8 <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_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.124.
* jfjoch_broker: Rotation indexer has two retries if failes
* jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot)
* jfjoch_broker: Integration calculates background mask based on R2 radius
* jfjoch_process: HDF5 files are not saved by default
Reviewed-on: #37
This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis.
If things go wrong with analysis, it is better to revert to 1.0.0-rc.124.
* jfjoch_broker: Improve logic on switching on/off spot finding
* jfjoch_broker: Increase maximum spot count for FFBIDX to 65536
* jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD)
* jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis
* jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection
* jfjoch_writer: Save more information about each reflection
Reviewed-on: #32
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them,
especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123.
* jfjoch_broker: Improve refection position prediction and Bragg integration code.
* jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation.
* jfjoch_writer: Fix saving mosaicity properly in HDF5 file.
* jfjoch_viewer: Introduce high-dynamic range mode for images
* jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%)
* jfjoch_viewer: Zoom-in numbers have better readability
Reviewed-on: #31
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_f