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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
141 lines
7.1 KiB
C++
141 lines
7.1 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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#include <cstring>
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#include "bitshuffle/bitshuffle.h"
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#include "FrameTransformation.h"
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#include "../common/RawToConvertedGeometry.h"
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#include "../common/JFJochException.h"
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template <class T> void FillVector(std::vector<char> &v, int64_t fill_value) {
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auto ptr = (T *) v.data();
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for (int i = 0; i < v.size() / sizeof(T); i++)
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ptr[i] = static_cast<T>(fill_value);
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}
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FrameTransformation::FrameTransformation(const DiffractionExperiment &in_experiment) :
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experiment(in_experiment),
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image_mode(in_experiment.GetImageMode()),
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pixel_depth(in_experiment.GetByteDepthImage()),
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compressor(in_experiment.GetCompressionAlgorithm()),
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err_value(experiment.GetByteDepthImage() * RAW_MODULE_SIZE) {
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precompression_buffer.resize(experiment.GetPixelsNum() * pixel_depth);
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switch (image_mode) {
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case CompressedImageMode::Int8:
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FillVector<int8_t>(precompression_buffer, experiment.GetImageFillValue());
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FillVector<int8_t>(err_value, experiment.GetImageFillValue());
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break;
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case CompressedImageMode::Int16:
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FillVector<int16_t>(precompression_buffer, experiment.GetImageFillValue());
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FillVector<int16_t>(err_value, experiment.GetImageFillValue());
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break;
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case CompressedImageMode::Int32:
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FillVector<int32_t>(precompression_buffer, experiment.GetImageFillValue());
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FillVector<int32_t>(err_value, experiment.GetImageFillValue());
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break;
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case CompressedImageMode::Uint8:
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FillVector<uint8_t>(precompression_buffer, experiment.GetImageFillValue());
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FillVector<uint8_t>(err_value, experiment.GetImageFillValue());
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break;
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case CompressedImageMode::Uint16:
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FillVector<uint16_t>(precompression_buffer, experiment.GetImageFillValue());
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FillVector<uint16_t>(err_value, experiment.GetImageFillValue());
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break;
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case CompressedImageMode::Uint32:
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FillVector<uint32_t>(precompression_buffer, experiment.GetImageFillValue());
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FillVector<uint32_t>(err_value, experiment.GetImageFillValue());
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image mode not supprted for FrameTransformation");
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}
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}
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size_t FrameTransformation::CompressImage(void *output, size_t output_size) {
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return compressor.Compress(output, output_size, precompression_buffer.data(), experiment.GetPixelsNum(),
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experiment.GetByteDepthImage());
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}
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CompressedImage FrameTransformation::GetCompressedImage() {
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const uint8_t *data;
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size_t size;
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if (experiment.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION) {
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data = reinterpret_cast<uint8_t *>(precompression_buffer.data());
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size = experiment.GetPixelsNum() * experiment.GetByteDepthImage();
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} else {
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compressed_buffer.resize(MaxCompressedSize(experiment.GetCompressionAlgorithm(),
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experiment.GetPixelsNum(),
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experiment.GetByteDepthImage()));
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data = reinterpret_cast<uint8_t *>(compressed_buffer.data());
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size = CompressImage(compressed_buffer.data(), compressed_buffer.size());
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}
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return CompressedImage(data, size,experiment.GetXPixelsNum(),
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experiment.GetYPixelsNum(), image_mode,
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experiment.GetCompressionAlgorithm());
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}
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void FrameTransformation::ProcessModule(const void *input, uint16_t module_number, int data_stream) {
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size_t module_number_abs = experiment.GetFirstModuleOfDataStream(data_stream) + module_number;
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if (!experiment.IsGeometryTransformed()) {
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size_t mod_size = RAW_MODULE_SIZE * pixel_depth;
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memcpy(precompression_buffer.data() + module_number_abs * mod_size, input, mod_size);
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} else {
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auto pixel0 = experiment.GetPixel0OfModuleConv(module_number_abs);
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auto fast_step = experiment.GetModuleFastDirectionStep(module_number_abs);
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auto slow_step = experiment.GetModuleSlowDirectionStep(module_number_abs);
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switch (image_mode) {
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case CompressedImageMode::Int8:
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TransferModuleAdjustMultipixels((int8_t *) precompression_buffer.data(), (int8_t *) input,
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slow_step, static_cast<int8_t>(INT8_MIN), static_cast<int8_t>(INT8_MAX),
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fast_step, pixel0);
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break;
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case CompressedImageMode::Int16:
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TransferModuleAdjustMultipixels((int16_t *) precompression_buffer.data(), (int16_t *) input,
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slow_step, static_cast<int16_t>(INT16_MIN), static_cast<int16_t>(INT16_MAX),
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fast_step, pixel0);
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break;
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case CompressedImageMode::Int32:
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TransferModuleAdjustMultipixels((int32_t *) precompression_buffer.data(), (int32_t *) input,
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slow_step, static_cast<int32_t>(INT32_MIN), static_cast<int32_t>(INT32_MAX),
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fast_step, pixel0);
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break;
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case CompressedImageMode::Uint8:
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TransferModuleAdjustMultipixels((uint8_t *) precompression_buffer.data(), (uint8_t *) input,
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slow_step, static_cast<uint8_t>(0), static_cast<uint8_t>(UINT8_MAX - 1),
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fast_step, pixel0);
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break;
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case CompressedImageMode::Uint16:
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TransferModuleAdjustMultipixels((uint16_t *) precompression_buffer.data(), (uint16_t *) input,
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slow_step, static_cast<uint16_t>(0), static_cast<uint16_t>(UINT16_MAX - 1),
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fast_step, pixel0);
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break;
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case CompressedImageMode::Uint32:
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TransferModuleAdjustMultipixels((uint32_t *) precompression_buffer.data(), (uint32_t *) input,
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slow_step, static_cast<uint32_t>(0), static_cast<uint32_t>(UINT32_MAX - 1),
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fast_step, pixel0);
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image mode not supprted for FrameTransformation");
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}
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}
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}
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void FrameTransformation::ProcessModule(const DeviceOutput *output, int data_stream) {
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ProcessModule(output->pixels, output->module_statistics.module_number, data_stream);
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}
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const void *FrameTransformation::GetImage() const {
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return precompression_buffer.data();
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}
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void FrameTransformation::FillNotCollectedModule(uint16_t module_number, int data_stream) {
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ProcessModule(err_value.data(), module_number, data_stream);
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}
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