A pin, loop or capillary on the goniometer shadows one place for part of the rotation only. The
beam-stop mask is one for every frame and is read off the mean over the pre-scan sample, so a pixel
such hardware covers on fewer than about half the sampled frames is kept and integrated attenuated
on the frames it is covered on. Since the pre-scan samples only the first part of the sweep (part B,
5b9144410), a sweep whose moving shadow is short in the first half and long in the second loses it:
on the in-house half-image lysozyme sweep the mask fell from 32.8% to 21.6% of the detector, the
second half of the sweep was integrated through the shadow, ISa dropped 6.9 -> 4.1, R_meas 116 ->
240%, the cell refined a != b, and the attenuated intensities erased the a-axis screw evidence
(merged rc175: P4_1 2 2 instead of P4_1 2_1 2).
The sample is now also read in blocks of 10 consecutive frames (rotation only); each block's shadow
is found on its own with the rings about the whole sample's centre, and the blocks' pieces that
reach beyond the 30 px band the whole sample's edge can grow over (PENUMBRA_MAX_PX) are added whole.
A pixel shadowed on most frames of any longer stretch is shadowed on most frames of one block, so
nothing finer is needed; pieces within the band are a block redrawing a static stop's edge and are
left out, so a sweep without moving hardware keeps its mask bit for bit. Part B's principle is kept:
everything is still decided on the first part of the sweep.
Measured (GPU, against merged rc175 eac0833c8, 19 sets): half-image lysozyme P4_1 2_1 2, ISa 4.1 ->
9.7, R_meas 240 -> 113%, CC1/2 0.955 -> 0.979, R-free(model) 0.331 -> 0.282 (last night 6.9 / 116%).
p.mtz md5-identical on 14 of 19 (8v4o, 9rci, 5ky6, 6yqf, 6ze4, 5reo, 9qw8, insu_I low-ISa,
insu_H notwin, myob powder 1/2, myob split, nothing_1/2); changed: 5nw5 (a dim crescent at the stop
edge now masked: ISa 8.4 -> 8.9, CC1/2 0.937 -> 0.980, R-free 0.462 -> 0.429), 7atg (0.85% added at
the detector edge, statistics unchanged), 9min (0.03%, fail -> fail unchanged), 5jk4 (<0.01%,
unchanged). Cost: pre-scan +0.1 s on HDF5 sweeps, +1-5 s on large file-per-image (CBF, marCCD)
sweeps, where the blocks are re-read and their masks computed on the host.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
leonarski_fandClaude Opus 5.5
f257d51ea6
