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Jungfraujoch/receiver/FrameTransformation.cpp
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leonarski_f d6389e12da
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v1.0.0-rc.156 (#66)
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>
2026-07-03 19:18:56 +02:00

141 lines
7.1 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <cstring>
#include "bitshuffle/bitshuffle.h"
#include "FrameTransformation.h"
#include "../common/RawToConvertedGeometry.h"
#include "../common/JFJochException.h"
template <class T> void FillVector(std::vector<char> &v, int64_t fill_value) {
auto ptr = (T *) v.data();
for (int i = 0; i < v.size() / sizeof(T); i++)
ptr[i] = static_cast<T>(fill_value);
}
FrameTransformation::FrameTransformation(const DiffractionExperiment &in_experiment) :
experiment(in_experiment),
image_mode(in_experiment.GetImageMode()),
pixel_depth(in_experiment.GetByteDepthImage()),
compressor(in_experiment.GetCompressionAlgorithm()),
err_value(experiment.GetByteDepthImage() * RAW_MODULE_SIZE) {
precompression_buffer.resize(experiment.GetPixelsNum() * pixel_depth);
switch (image_mode) {
case CompressedImageMode::Int8:
FillVector<int8_t>(precompression_buffer, experiment.GetImageFillValue());
FillVector<int8_t>(err_value, experiment.GetImageFillValue());
break;
case CompressedImageMode::Int16:
FillVector<int16_t>(precompression_buffer, experiment.GetImageFillValue());
FillVector<int16_t>(err_value, experiment.GetImageFillValue());
break;
case CompressedImageMode::Int32:
FillVector<int32_t>(precompression_buffer, experiment.GetImageFillValue());
FillVector<int32_t>(err_value, experiment.GetImageFillValue());
break;
case CompressedImageMode::Uint8:
FillVector<uint8_t>(precompression_buffer, experiment.GetImageFillValue());
FillVector<uint8_t>(err_value, experiment.GetImageFillValue());
break;
case CompressedImageMode::Uint16:
FillVector<uint16_t>(precompression_buffer, experiment.GetImageFillValue());
FillVector<uint16_t>(err_value, experiment.GetImageFillValue());
break;
case CompressedImageMode::Uint32:
FillVector<uint32_t>(precompression_buffer, experiment.GetImageFillValue());
FillVector<uint32_t>(err_value, experiment.GetImageFillValue());
break;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image mode not supprted for FrameTransformation");
}
}
size_t FrameTransformation::CompressImage(void *output, size_t output_size) {
return compressor.Compress(output, output_size, precompression_buffer.data(), experiment.GetPixelsNum(),
experiment.GetByteDepthImage());
}
CompressedImage FrameTransformation::GetCompressedImage() {
const uint8_t *data;
size_t size;
if (experiment.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION) {
data = reinterpret_cast<uint8_t *>(precompression_buffer.data());
size = experiment.GetPixelsNum() * experiment.GetByteDepthImage();
} else {
compressed_buffer.resize(MaxCompressedSize(experiment.GetCompressionAlgorithm(),
experiment.GetPixelsNum(),
experiment.GetByteDepthImage()));
data = reinterpret_cast<uint8_t *>(compressed_buffer.data());
size = CompressImage(compressed_buffer.data(), compressed_buffer.size());
}
return CompressedImage(data, size,experiment.GetXPixelsNum(),
experiment.GetYPixelsNum(), image_mode,
experiment.GetCompressionAlgorithm());
}
void FrameTransformation::ProcessModule(const void *input, uint16_t module_number, int data_stream) {
size_t module_number_abs = experiment.GetFirstModuleOfDataStream(data_stream) + module_number;
if (!experiment.IsGeometryTransformed()) {
size_t mod_size = RAW_MODULE_SIZE * pixel_depth;
memcpy(precompression_buffer.data() + module_number_abs * mod_size, input, mod_size);
} else {
auto pixel0 = experiment.GetPixel0OfModuleConv(module_number_abs);
auto fast_step = experiment.GetModuleFastDirectionStep(module_number_abs);
auto slow_step = experiment.GetModuleSlowDirectionStep(module_number_abs);
switch (image_mode) {
case CompressedImageMode::Int8:
TransferModuleAdjustMultipixels((int8_t *) precompression_buffer.data(), (int8_t *) input,
slow_step, static_cast<int8_t>(INT8_MIN), static_cast<int8_t>(INT8_MAX),
fast_step, pixel0);
break;
case CompressedImageMode::Int16:
TransferModuleAdjustMultipixels((int16_t *) precompression_buffer.data(), (int16_t *) input,
slow_step, static_cast<int16_t>(INT16_MIN), static_cast<int16_t>(INT16_MAX),
fast_step, pixel0);
break;
case CompressedImageMode::Int32:
TransferModuleAdjustMultipixels((int32_t *) precompression_buffer.data(), (int32_t *) input,
slow_step, static_cast<int32_t>(INT32_MIN), static_cast<int32_t>(INT32_MAX),
fast_step, pixel0);
break;
case CompressedImageMode::Uint8:
TransferModuleAdjustMultipixels((uint8_t *) precompression_buffer.data(), (uint8_t *) input,
slow_step, static_cast<uint8_t>(0), static_cast<uint8_t>(UINT8_MAX - 1),
fast_step, pixel0);
break;
case CompressedImageMode::Uint16:
TransferModuleAdjustMultipixels((uint16_t *) precompression_buffer.data(), (uint16_t *) input,
slow_step, static_cast<uint16_t>(0), static_cast<uint16_t>(UINT16_MAX - 1),
fast_step, pixel0);
break;
case CompressedImageMode::Uint32:
TransferModuleAdjustMultipixels((uint32_t *) precompression_buffer.data(), (uint32_t *) input,
slow_step, static_cast<uint32_t>(0), static_cast<uint32_t>(UINT32_MAX - 1),
fast_step, pixel0);
break;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image mode not supprted for FrameTransformation");
}
}
}
void FrameTransformation::ProcessModule(const DeviceOutput *output, int data_stream) {
ProcessModule(output->pixels, output->module_statistics.module_number, data_stream);
}
const void *FrameTransformation::GetImage() const {
return precompression_buffer.data();
}
void FrameTransformation::FillNotCollectedModule(uint16_t module_number, int data_stream) {
ProcessModule(err_value.data(), module_number, data_stream);
}