leonarski_fandClaude Opus 4.8
0ed50d91c9
The offline CPU spot finder marks a pixel strong when it clears a fixed photon
count AND a local-window SNR. The fixed photon floor forces per-dataset tuning:
its sweet spot tracks the background level (weak sets want a low threshold,
strong or high-background sets a high one) and the usable window is narrow, so
users hand-tune --spot-threshold/--spot-sigma per dataset.
Add an opt-in --adaptive-spots mode (AdaptiveSpotFinderCPU) that replaces the
fixed floor with a per-resolution-ring threshold derived from each image's own
noise. Per ring it computes a peak-excluded background mean and sigma (one plain
pass + two sigma-clip passes over the assembled photon image, binned by the
azimuthal-integration ring index) and sets
thr = max( PoissonTail(mean, p), mean + z * sqrt(sigma^2 + read^2) )
with p = false_pixels_per_frame / n_pixels the single portable knob (default
100) and z = Phi^-1(1 - p). The Poisson arm is the correct significance where
the background is countable (it carries the sqrt(mean) shot noise, so a bright
low-resolution ring gets a high threshold); the read-noise-floored Gaussian arm
keeps the threshold physical where the background vanishes (empty high-resolution
rings), without which those rings flood. read is a detector-level constant, not
a per-dataset knob. Both arms are needed: Poisson alone floods near-zero
background, Gaussian alone drops the shot-noise term and under-thresholds bright
rings.
One --adaptive-spots setting then adapts across a wide range of serial datasets
with no per-dataset threshold, matching or beating hand-tuned thresholds and the
peakfinder8/xgandalf reference on both weak large-cell and strong serial data,
with equal merged R-free.
The finder runs on the CPU (offline/viewer path) and reads the host image, which
the GPU pipeline already keeps in sync, so it works in either build. The default
(non-adaptive) path and the online/FPGA path are unchanged.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.