leonarski_fandClaude Opus 5
4d3434e2a5
The background belongs to the beam and the shadow to the stop, and the two are not concentric - fitting the stop edge per azimuth gives offsets of 13.4 px on an 85.8 px disk, 22.2 px on 67.3 px and 6.9 px on 23.7 px, 8 to 33 per cent of the stop radius on every crystal measured. The finder bridged that gap with a radial envelope, the largest ring background over an outward window, used as the reference for an individual pixel. That quantity exceeds the local background wherever the background rises outward, so sound pixels near the stop scored below the penumbra threshold and were masked. Measured against the fitted edge on a long-distance disk stop, the mask was displaced rather than mis-sized: short by up to 20 px on one side, over-reaching by up to 45 px on the other, with eight of twenty-four azimuth sectors falling short. The ring median is already the right reference wherever a ring still has unshadowed pixels to measure, which is every ring except those lying wholly inside the disk - and it needs no assumption about where the stop sits. So the envelope is gone from the per-pixel test, and the rings it existed to cover are handled directly: walking outward, a ring whose background is a fraction of the background further out is shadow in its entirety. That comparison is only ever asked whether a whole ring is inside the stop, never to judge a pixel, which is where its failure mode lives. Blockage is deliberately not a counting test - on a bright dataset the shadow interior is still well counted. Detection is now one channel instead of two, and 113 lines shorter. Measured: no azimuth sector falls short by more than 3.4 px, over-reach drops on all three fitted crystals, and mask area moves by at most 0.04 per cent of the detector on six crystals, so this corrects the shape rather than resizing. Battery: space-group agreement with XDS unchanged at 34/37, median change in R_meas and in the lowest shell 0.000 pp. The crystal that suffered worst when masking was introduced recovers to its unmasked quality - R_meas 25.1 -> 17.2 per cent, ISa 4.45 -> 10.04 - which is what removing the over-masking should do. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
64 lines
2.7 KiB
C++
64 lines
2.7 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <cstdint>
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#include <mutex>
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#include <vector>
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#include "../../common/CompressedImage.h"
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#include "../../common/DiffractionExperiment.h"
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#include "../../common/JFJochMessages.h"
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#include "../../common/PixelMask.h"
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// Finds the beam-stop shadow - the central disk and the holder arm - from a set of images,
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// mirroring the accumulate-then-finalize shape of DarkMaskAnalysis: feed frames with
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// AddImage(), then read the mask once with GetMask(). The mask is in converted geometry
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// and is 1 where the beam stop shadows the detector.
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//
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// The shadow is a place where the background is missing, so it is found by comparing each
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// pixel's mean against the typical background at the same radius - the median over its ring,
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// taken over the pixels not already known to be shadowed. That comparison holds wherever the
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// ring still has unshadowed pixels to measure. Where it does not - a ring lying wholly inside
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// the stop - there is nothing to compare against, and such a ring is shadow in its entirety.
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//
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// The background belongs to the beam and the shadow to the stop, and the two are not concentric:
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// the stop sits off the beam by a sizeable fraction of its own radius. Only the per-ring
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// comparison is used, so nothing here assumes they share a centre.
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//
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// Frames are chosen by the caller; the detection needs enough of them that the background
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// is counted rather than guessed (see MIN_EXPECTED_COUNTS in the .cpp).
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// Thread-safe: AddImage may be called from several worker threads.
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class ShadowFinder {
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mutable std::mutex m;
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const int width;
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const int height;
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const float beam_x;
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const float beam_y;
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std::vector<uint32_t> pixel_mask; // pixels already masked carry no background to test
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// Per-pixel projection over the frames added so far (converted geometry).
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std::vector<int64_t> max_value;
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std::vector<int64_t> sum_value;
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std::vector<uint32_t> valid_count;
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uint32_t frames = 0;
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template<class T> void Add(const T *ptr);
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public:
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ShadowFinder(const DiffractionExperiment &experiment, const PixelMask &mask);
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// Accumulate one full converted-geometry image. Gap / masked pixels (the pixel type's
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// sentinel extreme) are skipped. `buffer` is scratch space for decompression.
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void AddImage(const DataMessage &data, std::vector<uint8_t> buffer);
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// Compute the shadow mask (1 = shadow, 0 = keep), of the converted pixel count.
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// Recomputed from the accumulators on each call - meant to be called once at the end.
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[[nodiscard]] std::vector<uint32_t> GetMask() const;
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[[nodiscard]] uint32_t GetFrameCount() const;
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};
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