leonarski_fandClaude Opus 5.5
12d6208126
The pixels rugnux measures as outside a CCD's active area shared bit 1 with the detector's own bad
pixels, so they could not be told from the device mask and pixel_sum left them out. They now have bit 11,
a run-determined bit like the shadow and the hot pixels: they stay masked in the image and the other
statistics, and pixel_sum counts them. The beam-stop finder still reads them as data.
A file written with this mask no longer shows them as bit 1. The jfjoch XDS plugin and DIALS mask any
bit, so they still mask them; Durin and Neggia, which ignore the bits from 8 up, no longer do.
(ported from rc184-2 e6baecda5)
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAK
94 lines
5.0 KiB
C++
94 lines
5.0 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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// One byte per pixel, non-zero where the pixel is masked at all (see BinaryMaskDevice) - the form
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// the GPU image preprocessor uploads - and the checksum the shared device-table cache keys on (CudaSharedTables.h). Both are
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// pure functions of `mask`, and an analysis engine is built per worker per pass, so they are
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// derived here once instead of in every one of those engines.
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std::vector<uint8_t> binary_mask;
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uint64_t binary_mask_checksum = 0;
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// The same flag packed 32 pixels to a word (pixel i is bit i % 32 of word i / 32) - the form the CPU
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// image preprocessor reads, derived here for the same reason.
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std::vector<uint32_t> packed_mask;
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// Packed the same way: the pixels masked only by what a run found on its own frames.
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std::vector<uint32_t> packed_run_mask;
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uint32_t LoadMask(const std::vector<uint32_t>& mask, uint8_t bit);
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// Everything that follows from the mask, recomputed wherever the mask changes.
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void UpdateDerived(const DiffractionExperiment& experiment);
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void UpdateBinaryMask();
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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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// Found bad on the run's own frames (rugnux pre-scan, HotPixelFinder): lit above its ring on too
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// many frames, or holding the error value on most of them.
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constexpr static const uint8_t HotPixelBit = 10;
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// Outside a CCD's active area, measured on the run's own frames (RugnuxMeasuredGain::constant).
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constexpr static const uint8_t InactivePixelBit = 11;
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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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// What a run determines on its own frames, as against the detector's and the calibration's mask.
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constexpr static const uint32_t RunMaskBits = (1u << BeamStopPixelBit) | (1u << HotPixelBit)
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| (1u << InactivePixelBit);
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// The values of GetBinaryMask(): masked by the device mask, or only by what the run determined.
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constexpr static const uint8_t BinaryMaskDevice = 1;
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constexpr static const uint8_t BinaryMaskRunOnly = 2;
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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 LoadHotPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
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// Pixels that record nothing (InactivePixelBit), added to whatever the bit already holds.
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void AddDeadPixelMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
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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]] const std::vector<uint8_t> &GetBinaryMask() const;
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[[nodiscard]] const std::vector<uint32_t> &GetPackedMask() const;
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[[nodiscard]] const std::vector<uint32_t> &GetPackedRunMask() const;
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[[nodiscard]] uint64_t GetBinaryMaskChecksum() 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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