Two defects the merge created and one the API carried.
Rugnux gated the per-image spot engine on AnalysisModeIsMX, so AnalysisMode::Grid
fell through to the azimuthal-integration-only path: a raster ran, scored nothing,
and reported no crystals. The gate now asks the stages table whether the mode does
spot finding, which is the actual question - three modes need that engine for three
different reasons, and a fourth would otherwise have to be remembered here too.
max_crystals was a required integer defaulting to 10, with 0 meaning "all". Zero
reads as "report no crystals", the opposite of what it did. It is now optional, and
absent means no cap; a crystal found and then dropped is information the caller
cannot get back. grow_score_threshold was missing from the schema entirely.
Measured over the labelled corpus after these fixes: 34 of 34 confirmed-protein
rasters yield a crystal, 0 of 8 water, 0 of 6 ice, 19 of 19 heldout.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
A crystal in the corpus was reported as two because the grid point joining its halves
scored 0.498 - two thousandths under the threshold. That is an artefact of putting a
hard edge through a continuous quantity, not a gap in a crystal.
The patch search is now hysteresis. A patch is labelled at a lower grow threshold
(0.35) and kept only if it holds a cell above the seed threshold (0.50), which is the
same thing as growing out of the seeds in one pass of the labeller rather than two. A
cell between the two levels joins a crystal that already exists but can never start
one, so no lowering of the grow threshold can turn a background into a crystal - and
the negatives are safe by construction, since water peaks at 0.146 and ice at 0.490,
both under the seed level.
Both halves of the small-patch rule read the GROWN patch - the count includes the
cells growth added and the peak is the patch's best cell wherever it lies - which is
stated at the test, because a reader will otherwise wonder whether a grown cell can
rescue a patch no seed would have admitted. It cannot: the patch is discarded before
that test unless it holds a seed.
The reported extents are those of the grown patch, so they reach the 0.35 contour. Over
the corpus that is major_um x1.04 and n_images x1.07 at the median (x1.11 and x1.14 at
the mean, +7% cells overall), and the cells it adds are spread fairly evenly over
0.35-0.50 rather than piled at the bottom - a crystal edge sampled at one grid step, not
bleed into a neighbour that never diffracted. The patch mean falls with them, and can now
sit below the seed threshold; the peak beside it is what the admission was decided on.
RASTER_REPORT_VERSION is 3, because N_CELLS and the extents are a different measurement
under the same names.
The corpus table is unchanged: 17/17 protein, 0/4 water, 0/3 ice, 10/10 heldout. The
split heals into one crystal, and one raster's five patches become three.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
The minimum patch size was a flat floor, so a crystal that covers one or two grid
points was thrown away however strong its diffraction. It is now a floor OR a piece
of evidence: a patch is reported when it has min_blob_cells cells, or when its best
cell reaches decisive_protein_score. One condition, and both halves are parameters.
The bar is the patch PEAK, not the patch mean. A two-cell patch with one strong cell
and one marginal one is the case this exists for, and the mean averages exactly that
evidence away. Over the 67 labelled rasters the two populations do not overlap: no
water raster reaches a peak of 0.15 and no ice raster reaches 0.50, while the weakest
protein raster peaks at 0.67 - so 0.6, the middle of that gap, is the default. The
peak is reported beside the mean, in the table and in the JSON, so an admission can
be checked against the number that decided it.
max_crystals caps the returned list after the sort, best first; 0, the default, is all
of them, because a crystal that was found and then dropped is information the caller
cannot get back.
The four parameters now travel as one GridScanAnalysisParameters, which is the shape
the GridScanAnalysisSettings class in common/ is to take: when it lands it replaces
this struct in the signature and nothing else changes.
On the corpus this reaches 17/17 protein loops (it was 16/17 - the miss was a crystal
covering two grid points of a 4x4 raster) with water still 0/4 and ice still 0/3.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
The offline entry point for a raster. It scores every image of a stored grid scan
- spot finding for the per-cell resolution, no indexing, because a raster answers
where the crystal is and not what its lattice is - hands the per-image protein and
ice scores to AnalyzeGridScan, and writes what came back as two files beside the
usual output: <prefix>_raster_report.txt in the idiom of the results report, and
<prefix>_raster.json with the same content typed, so a battery can aggregate a
sweep without scraping prose.
--beam-size states the beam at the sample, defaulting to the file's
incident_beam_size. It matters more than it looks: the reported crystal sizes are
measured and still contain the beam, and taking an anisotropic beam back out is a
subtraction of two covariance matrices, so a beam given as square when it is not
rotates the reported crystal axis. --raster-protein-threshold and
--raster-min-cells expose the two constants AnalyzeGridScan held at file scope, so
a sweep can vary them without a rebuild; they are now defaulted parameters with the
old values, and every existing call is unchanged.
The observer feeding the analysis reads the file's own image number
(DataMessage::original_number), not the loop's ordinal, so -s/-e/--stride cannot
silently shift the grid mapping.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5