leonarski_f
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* rugnux is substantially faster - a corpus of 145 rotation datasets processes in about two thirds of the time - with identical results. * A crystal whose lattice looks more symmetric than it is because the beam centre is off is no longer processed on the wrong cell. * rugnux prints at startup, and writes at the foot of every results report, a short acknowledgement of the X-ray research community whose methods it implements and of the open-source projects it builds on; `ACKNOWLEDGEMENT.md` now ships in every package beside `LICENSE` and `THIRD_PARTY_NOTICES.md`. Reviewed-on: #78 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
92 lines
3.3 KiB
C++
92 lines
3.3 KiB
C++
// SPDX-FileCopyrightText: 2025 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 <vector>
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#include <unordered_set>
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#include <map>
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#include <mutex>
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#include <optional>
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#include "../common/TopPixels.h"
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#include "JFJochReaderDataset.h"
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#include "../common/CrystalLattice.h"
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#include "../common/Histogram.h"
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// Markers stored in place of an intensity. They occupy the bottom of the int32 range and
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// INT32_MAX at the top, so anything in between is a real count. Add a marker at the BOTTOM and move
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// MIN_REAL_PXL_VALUE with it - several places classify a pixel by range rather than by equality,
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// and they all test against MIN_REAL_PXL_VALUE.
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constexpr static int32_t ERROR_PXL_VALUE = INT32_MIN;
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constexpr static int32_t GAP_PXL_VALUE = INT32_MIN + 1;
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constexpr static int32_t BEAM_STOP_PXL_VALUE = INT32_MIN + 2;
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constexpr static int32_t MIN_REAL_PXL_VALUE = INT32_MIN + 3;
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constexpr static int32_t SATURATED_PXL_VALUE = INT32_MAX;
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struct JFJochReaderRawImage {
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RawByteBuffer image_buffer;
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CompressedImage image;
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// Scratch the reader needs to produce the image and that nothing else reads: the CBF reader
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// reads the compressed file into it before decoding. It lives here so that a raw image reused
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// from one frame to the next reuses this buffer too.
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std::vector<uint8_t> read_buffer;
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};
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class JFJochReaderImage {
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std::shared_ptr<const JFJochReaderDataset> dataset;
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std::vector<int32_t> image; // Image in the reader must be 32-bit signed, uncompressed
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DataMessage message;
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std::unordered_set<int64_t> saturated_pixel;
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std::unordered_set<int64_t> error_pixel;
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std::vector<std::pair<int32_t, int32_t>> valid_pixel;
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// Fast stats without storing/sorting all valid pixels
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int32_t valid_min = 0;
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int32_t valid_max = 0;
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size_t valid_count = 0;
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bool has_valid = false;
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// For overlay: track top pixels with a tiny O(K) structure; export to vector for UI
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TopPixels top_pixels_acc{20};
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std::vector<std::pair<int32_t, int32_t>> top_pixels;
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// This histogram operates in square root of count from 0 to 10^20
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Histogram count_histogram{100000};
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constexpr static float auto_foreground_range = 99.0f;
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int32_t auto_foreground;
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void CalcAutoContrast();
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template <class T>
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void ProcessInputImage(const void* image, size_t npixel, int64_t sat_value, int64_t special_value);
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void ProcessInputImage(const CompressedImage& image);
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public:
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JFJochReaderImage(const DataMessage &msg, const std::shared_ptr<const JFJochReaderDataset> &dataset);
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JFJochReaderImage(const JFJochReaderImage &other);
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const DataMessage &ImageData() const;
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DataMessage &ImageData();
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const std::vector<int32_t> &Image() const;
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const std::unordered_set<int64_t> &SaturatedPixels() const;
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const std::unordered_set<int64_t> &ErrorPixels() const;
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const JFJochReaderDataset &Dataset() const;
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std::optional<std::pair<int32_t, int32_t>> ValidMinMax() const;
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const std::vector<std::pair<int32_t, int32_t>> &GetTopPixels() const;
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void AddImage(const JFJochReaderImage& other);
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std::vector<float> GetAzInt1D() const;
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std::vector<float> GetAzInt1D_BinToQ() const;
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std::shared_ptr<JFJochReaderDataset> CreateMutableDataset();
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int32_t GetAutoContrastValue() const;
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std::vector<float> GetHistogram() const;
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};
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