leonarski_fandClaude Opus 5
a29c36600f
rugnux finds the beam stop and its holder in a projection of 60 images and marks them in the pixel mask as bit 9 (--detect-beam-stop[=N|off], on by default). Reflections behind the stop are attenuated but not flagged, so they integrate low with a plausible sigma and nothing downstream catches them: the signal-box gate requires 100% valid pixels and shadow pixels are valid, the background clip is high-side only, and the |zeta| cut applies only to the space-group search merge. The detection compares each pixel's background against the typical background at the same radius on two channels. An azimuthal one (the ring median) finds the holder arm, which is a minority of its ring; a radial one (the background just outside) finds the disk, which the ring median cannot see because inside a fully blocked ring the median is the shadow itself. Pixels are pooled over a 5x5 box and tested only where the background has actually been counted, so low-background data no longer masks the whole detector. Recorded reflections are carved back out - a beam stop cannot block a reflection that was measured. Bit 9 belongs to the run that found it, not to the dataset: it is cleared when a run starts, so a mask read back from a file that carries one starts clear. The user mask (bit 8) is left alone. Scaling and merging gain a low-resolution limit, default 50 A (--scaling-low-resolution <num>, 0 removes it), applied per observation before scaling so it also protects the per-frame scale fit and the space-group search. 50 A is the value XDS configurations use; rugnux_vs_xds.py now matches both of XDS's resolution limits instead of only the high one, so the lowest shell is the same shell in the two programs. The viewer draws the detected shadow in coral with a "Show beam stop" switch in the side panel, exposes the low-resolution limit in the settings dock, and offers detection in its processing jobs. Adding an image marker meant giving the reader a MIN_REAL_PXL_VALUE, because several places classify a pixel by range rather than by equality and would otherwise read the new marker as a very negative intensity. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
63 lines
2.7 KiB
C++
63 lines
2.7 KiB
C++
// SPDX-FileCopyrightText: 2024 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 "CompressedImage.h"
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#include "DetectorSetup.h"
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#include "DiffractionExperiment.h"
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#include "../jungfrau/JFCalibration.h"
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struct PixelMaskStatistics {
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uint32_t user_mask;
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uint32_t noisy_pixel;
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uint32_t error_pixel;
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uint32_t chip_gap_pixel;
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uint32_t total_masked;
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uint32_t module_gap_pixel;
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};
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class PixelMask {
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std::vector<uint32_t> mask;
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std::vector<uint32_t> raw_mask;
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uint32_t LoadMask(const std::vector<uint32_t>& mask, uint8_t bit);
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void UpdateRawMask(const DiffractionExperiment& experiment);
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void CalcEdgePixels_i(const DiffractionExperiment& experiment);
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public:
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// NXmx bits
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constexpr static const uint8_t ModuleGapPixelBit = 0;
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constexpr static const uint8_t ErrorPixelBit = 1;
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constexpr static const uint8_t NoisyPixelBit = 4;
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constexpr static const uint8_t UserMaskedPixelBit = 8;
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constexpr static const uint8_t BeamStopPixelBit = 9;
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constexpr static const uint8_t ChipGapPixelBit = 31;
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constexpr static const uint8_t ModuleEdgePixelBit = 30;
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PixelMask();
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explicit PixelMask(size_t width, size_t height);
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explicit PixelMask(const DiffractionExperiment& experiment);
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explicit PixelMask(const std::vector<uint32_t> &mask);
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void CalcEdgePixels(const DiffractionExperiment& experiment);
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void LoadUserMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
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void LoadUserMask(const DiffractionExperiment& experiment, const CompressedImage& image);
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void LoadBeamStopMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
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// The beam-stop shadow belongs to the run that found it, not to the dataset, so a mask read back
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// from a file that carries one starts clear. The user mask (bit 8) is deliberately left alone.
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void ClearBeamStopMask(const DiffractionExperiment& experiment);
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void LoadDECTRISBadPixelMask(const std::vector<uint32_t>& mask);
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void LoadDarkBadPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
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void LoadDetectorBadPixelMask(const DiffractionExperiment& experiment, const JFCalibration *calib);
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[[nodiscard]] const std::vector<uint32_t> &GetMaskRaw() const;
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[[nodiscard]] const std::vector<uint32_t> &GetMask(const DiffractionExperiment& experiment) const;
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[[nodiscard]] const std::vector<uint32_t> &GetMask() const;
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[[nodiscard]] std::vector<uint32_t> GetUserMask(const DiffractionExperiment& experiment) const;
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[[nodiscard]] std::vector<uint32_t> GetUserMask() const;
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[[nodiscard]] PixelMaskStatistics GetStatistics() const;
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};
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