2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	5fe8a967cd	grid scan: the five lanes become one, with a single home for the crystal type and its settings ... Integration of the per-image detection scores, the analysis mode, the grid-scan crystal search, its rugnux entry point and the viewer display. GridScanCrystal/GridScanResult had two definitions - a placeholder in common/ and the real one in image_analysis/ - which is a redefinition in any translation unit reaching both, and tests/RasterReportTest.cpp reaches both. Unified into common/GridScanResult.h, beside ScanResult where the data type belongs, leaving the algorithm in image_analysis/. Same reason UnitCell lives in common while the indexers do not. GridScanAnalysisSettings is now the only home for the search parameters, replacing the loose GridScanAnalysisParameters struct the raster lane carried while the class did not yet exist. Three values changed with the move: - decisive_single_cell_score 0.9 -> 0.6. 0.9 drops a real two-cell crystal peaking at 0.751 and costs a loop on the labelled corpus. 0.6 is the middle of a measured gap: over 67 rasters no water raster peaks above 0.15 and no ice raster above 0.50, while the weakest confirmed-protein raster peaks at 0.67. - max_crystals is std::optional, unset meaning no cap. 0 as a sentinel for "unlimited" reads as "find nothing", which is the opposite of what it did. - grow_score_threshold was missing from the class entirely. The viewer reads protein_score, ice_score and the crystal list from the reader rather than a local stub, and asks the broker for ice_ring_ratio rather than the retired ice_ring_score spelling. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-08 07:59:04 +02:00
leonarski_fandClaude Opus 5	98132d0f83	analysis: every analysis method carries its own settings, and a raster's indexing is one of them ... AnalysisSettings had begun collecting per-method parameters - the calibrant was already in it, and the grid thresholds were about to be. That makes the structure every method reads grow whenever any one method gains a knob, and it puts a field in front of readers for whom it means nothing. So: AnalysisSettings keeps what all methods share, which for now is the mode, and each method gets a class of its own bound the same way. GridScanAnalysisSettings holds the protein-score threshold, the minimum cells per crystal, the decisive single-cell score, the maximum crystals reported and the indexing switch. CalibrationSettings holds the calibrant and the ring source. Both sit on DiffractionExperiment outside the per-run dataset member, both have an Import/Get pair, and both have their own endpoint - /config/grid_scan_analysis and /config/calibration - which is how every other settings group in this API is already reached. Grid indexing is no longer fixed in the stages table. It was turned off there on cost grounds, and that reasoning does not hold: a raster runs at up to 100 Hz, which the FFT indexer keeps up with, and a fixed-target serial experiment with a known cell wants ffbidx on every cell, where a raster that indexes is most of the measurement. So it is a setting, and DEFAULTS ON. It is additive rather than a change of answer - blobs are still found on the protein score, so indexing alters nothing about which cells are called crystals and only adds what was found in them, including the per-cell lattice count, which is the cheapest multi-lattice or cracked-crystal signal there is. That makes indexing the one stage a mode does not decide. AnalysisModeStages still carries a value for it, but only as the setting's default, and DiffractionExperiment::GetAnalysisStages - which is what every gate reads - substitutes the configured one. The table row is marked so nobody reads it as the mode's answer. The calibration knobs stay coupled to the mode but the rule now lives with them: CalibrationSettings::ApplyToAzimuthalIntegration moves azimuthal integration onto the CPU and supplies sectors where fewer than four were asked for, carrying the reason with it - the FPGA integration core holds 2048 bins in total, so 32 sectors leave 64 q bins, which cannot locate a ring. Stated there because it will otherwise read as an FPGA defect to be fixed back onto that path, and it is not one: the core is sized for a detector at full rate, and a calibration exposure is a few images at a few Hz. Both imports apply it, so the order the mode and the calibration settings are set in does not matter. CalibrationMethod moves from image_analysis/geom_refinement/PowderCalibration.h into common/CalibrationSettings.h, which that header now includes. One enum, so the setting and the code consuming it are not two vocabularies; every existing user sees it unchanged. The grid thresholds have one home and it is this class. The raster work owns AnalyzeGridScan's parameter surface and carries PROTEIN_SCORE_THRESHOLD_DEFAULT / MIN_BLOB_CELLS_DEFAULT beside that header today; the header here states the signature that replaces them, so the two do not become competing defaults. The beam size deliberately stays a separate argument to AnalyzeGridScan: it is measured, not configured. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-08 07:27:41 +02:00