3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	e381d2fd50	grid scan: review fixes - the ice channel sees its own spots, and a needle is not mirrored ... Two independent reviews of the merged grid-scan work. The findings that changed behaviour: The ice score's spot channel was fed a list the spot budget had already stripped. FilterSpotsByCount orders ice-band spots LAST when indexing is not to use them, so on a frame with more spots than the budget the ice spots are the first discarded - and the channel that exists for "ice arrives as discrete spots and leaves the radial profile flat" then read zero on exactly the frames it was written for. Probed at 3000 spots with 1200 on the hexagonal radii and a budget of 1000: 1.000 before the cap, 0.000 after. IceScore now takes d-spacings and is handed the list from before the cap. The viewer scaled the crystal box by the SIGNED grid step, where every other consumer takes the magnitude. On a negative step that mirrors the box - +30 deg drawn as -30 - and hands QRectF a negative width. rugnux --mode raster never put its settings on the experiment, so the indexing switch was read at its default while a deprecated per-run flag did the actual work; and RugnuxCommandLine emitted no --mode for Grid, so a raster job copied to a cluster ran the default mx - indexing, integrating and merging every cell of the raster. res_A is NaN where nothing in a blob measured a resolution, and nlohmann writes NaN as null, which the schema and the generated clients both reject. It is now left unset. The broker's configuration example named a key that does not exist (calibration, not calibration_settings); nlohmann ignores unknown keys, so a user copying it got a silently ignored block. The changelog had lost the rc.166 heading and 21 rc.167 entries to a bad edit of mine, and three entries had been filed under rc.166. Also: a warning where mode Grid meets a dataset with no grid scan, which was silent and indistinguishable from finding nothing; the viewer combo still named the retired ice_ring_score; and the claim that growth "cannot invent a crystal" was too strong - it cannot start a patch, but the cell count is read over the grown patch, so it does decide which patches pass. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-08 09:04:52 +02:00
leonarski_fandClaude Opus 5	0f00b76a9a	image analysis: the ice score takes the pipeline's own band width, and the ice quantities are named for what kind of number they are ... Two things, both about telling one ice quantity from another. The ice score's spot channel had its own band half-width of 0.02 A^-1 while the spot finder marks ice rings at 0.03 (ice_ring_width_Q_recipA). The 0.02 was justified by a 5 pp specificity gain measured on the PYTHON PROTOTYPE, which used a fitted beam centre and a mask-derived coverage table; the shipped port, which takes the geometry's centre and the azimuthal profile's own live pixel count, does not reproduce it. Measured over the corpus by truth class rather than by directory label, at 0.02 vs 0.03 on the combined score: ice loops 62.13/62.19%, _icy protein 89.03/89.79%, _clean protein 16.51/16.31%, water 17.19/20.03%. The widths are indistinguishable except on water, where one of the four loops is independently known to carry a full hexagonal pattern. So the width is now a parameter and the pipeline's own value is passed in - one band width, not two. The 0.012 tolerance in the radial channel is NOT a second band width, and is renamed CENTRE_SMEAR_Q to say so: it is how far either side the channel looks for the bin a mis-set beam centre moved the ring to. The rest is naming. Three kinds of number were all called score, or built from things called count, and a reader could not tell from the name whether 1 meant "none" or "certain" - which are opposite. The convention, now stated in docs/CPU_DATA_ANALYSIS.md: *_score is bounded [0,1] and 1 is certainty, *_ratio is unbounded and 1 is nothing, *_count is a count. The C++ identifiers for the ice ring ratio follow it (ice_ring_score -> ice_ring_ratio, GetIceRingScore -> GetIceRingRatio, PlotType::IceRingScore -> IceRingRatio), and the local in the scaling gate that shadowed the new ice_score while meaning the ring ratio is renamed with them. Nothing outside the source moved: the CBOR keys ice_ring_score and ice_ring_score_mean, the datasets /entry/MX/iceRingScore and iceRingScoreMean, the ice_ring_score plot type and the --ice-min-score flag are all unchanged, and were checked to be after the rename. Renaming those changes stored files, the stream format, the REST API and a CLI flag, and is a separate decision. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-08 07:19:03 +02:00
leonarski_fandClaude Opus 5	62ca2b24f6	image analysis: two per-image detection scores say whether there is protein and whether there is ice ... 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	2026-09-07 23:59:46 +02:00