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image analysis: two per-image detection scores say whether there is protein and whether there is ice

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proteinScore and iceScore are saturating scores in [0,1] that answer presence, not quality: a superb
crystal and a barely-diffracting one both read near 1, and neither the spot count nor the resolution
enters either of them as a term. iceRingScore already reports a magnitude - a ratio, unbounded - which
is not a number that can be thresholded; these are.

The protein score counts distinct d SHELLS above 5 A rather than spots, so a parasitic ring in the
low-resolution band cannot accumulate evidence, and weights each spot against the frame's own median
so a scattering of the weakest detections cannot fill a shell either. The ice score carries two
channels and takes the stronger: a radial one over the azimuthal profile, which runs the hexagonal
and the CUBIC phase as separate hypotheses and decides between them at the end (flash-cooled loops
show cubic or stacking-disordered ice at least as often as hexagonal, the two share only three
lines, and dropping the cubic hypothesis costs about 5 pp on iced loops), and a spot one that reads
an excess on the ice radii against the same band slid to every ice-free offset, which is what
catches ice arriving as discrete crystallites and leaving the radial profile flat.

Both read d out of the geometry, so both move with a beam-centre error; the centre is not fitted
here, and the one they were computed with is written beside them as scoreBeamCenterX/Y so a later
rescoring can tell an algorithm disagreement from a geometry one.

Ported from validated prototypes and checked against them frame by frame on stored data: mean
absolute difference 2.7e-5 (protein), 1.3e-8 (ice radial) and 3.4e-4 (ice spots). On a 41-loop
battery the protein score reaches 98.4% of confirmed-protein frames and 0.00% of water frames, and
finds no cluster on any water or ice raster. Cost is 0.01 ms/frame for the protein score and
0.08-0.32 ms/frame for the ice score.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
This commit is contained in:
leonarski_f
2026-09-07 23:59:46 +02:00
co-authored by Claude Opus 5
parent 680c36c20d
commit 62ca2b24f6
33 changed files with 960 additions and 1 deletions
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writer/HDF5DataFilePluginMX.cpp
+10
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@@ -54,6 +54,8 @@ HDF5DataFilePluginMX::HDF5DataFilePluginMX(const StartMessage &msg)
void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg, size_t images_per_file) {
bkg_estimate.reserve(images_per_file);
ice_ring_score.reserve(images_per_file);
protein_score.reserve(images_per_file);
ice_score.reserve(images_per_file);
if (max_spots == 0)
return;
@@ -101,6 +103,10 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
bkg_estimate[image_number] = msg.bkg_estimate.value();
if (msg.ice_ring_score.has_value())
ice_ring_score[image_number] = msg.ice_ring_score.value();
if (msg.protein_score.has_value())
protein_score[image_number] = msg.protein_score.value();
if (msg.ice_score.has_value())
ice_score[image_number] = msg.ice_score.value();
if (max_spots == 0)
return;
@@ -252,6 +258,10 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
data_file.SaveVector("/entry/MX/bkgEstimate", bkg_estimate.vec());
if (!ice_ring_score.empty())
data_file.SaveVector("/entry/MX/iceRingScore", ice_ring_score.vec());
if (!protein_score.empty())
data_file.SaveVector("/entry/MX/proteinScore", protein_score.vec());
if (!ice_score.empty())
data_file.SaveVector("/entry/MX/iceScore", ice_score.vec());
if (!profile_radius.empty())
data_file.SaveVector("/entry/MX/profileRadius", profile_radius.vec())->Units("Angstrom^-1");
if (!mosaicity_deg.empty())