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AcquisitionDevice: Setup rad. int. mapping automatically

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This commit is contained in:
leonarski_f
2023-10-20 18:00:29 +02:00
parent 7008703af3
commit 0b5bbec1fc
6 changed files with 165 additions and 1 deletions
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1
image_analysis/CMakeLists.txt
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@@ -3,6 +3,7 @@ ADD_LIBRARY(ImageAnalysis STATIC
IndexerWrapper.cpp IndexerWrapper.h
GPUImageAnalysis.h
RadialIntegration.cpp RadialIntegration.h
RadialIntegrationMappingFPGA.cpp RadialIntegrationMappingFPGA.h
RadialIntegrationMapping.cpp RadialIntegrationMapping.h
StrongPixelSet.cpp StrongPixelSet.h GPUImageAnalysis.cpp RadialIntegrationProfile.cpp RadialIntegrationProfile.h PredictSpotsOnDetector.h)

78
image_analysis/RadialIntegrationMappingFPGA.cpp Normal file
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@@ -0,0 +1,78 @@
// Copyright (2019-2023) Paul Scherrer Institute
#include <cmath>
#include "RadialIntegrationMappingFPGA.h"
#include "../common/RawToConvertedGeometry.h"
#include "../common/DiffractionGeometry.h"
RadialIntegrationMappingFPGA::RadialIntegrationMappingFPGA(const DiffractionExperiment &experiment, uint16_t data_stream) :
low_q(experiment.GetLowQForRadialInt_recipA()),
high_q(experiment.GetHighQForRadialInt_recipA()),
q_spacing(experiment.GetQSpacingForRadialInt_recipA()),
pixel_to_bin(experiment.GetModulesNum(data_stream) * RAW_MODULE_SIZE),
max_bin_number(0)
{
if (q_spacing < 0.0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Q-spacing has to be >= 0.0");
if (low_q >= high_q)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Low-Q must be smaller than high-Q");
if (low_q <= 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Low-Q must be > 0");
if (std::ceil((high_q-low_q) / q_spacing ) >= FPGA_INTEGRATION_BIN_COUNT)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Cannot accommodate more than " + std::to_string(FPGA_INTEGRATION_BIN_COUNT) + " rings");
for (int m = 0; m < experiment.GetModulesNum(data_stream); m++) {
for (int pxl = 0; pxl < RAW_MODULE_SIZE; pxl++) {
auto [x,y] = RawToConvertedCoordinate(experiment, m + experiment.GetFirstModuleOfDataStream(data_stream), pxl);
double pixel_q = 2 * M_PI / PxlToRes(experiment, x, y);
if ((pixel_q < low_q) || (pixel_q >= high_q))
pixel_to_bin[m * RAW_MODULE_SIZE + pxl] = UINT16_MAX;
else
pixel_to_bin[m * RAW_MODULE_SIZE + pxl] = std::floor((pixel_q - low_q) / q_spacing);
}
}
// In principle max bin number is equal to std::floor((high_q - low_q) / q_spacing), but it might be lower than this
// depending on detector distance and beam center position
for (const auto &i: pixel_to_bin) {
if ((i != UINT16_MAX) && (i > max_bin_number))
max_bin_number = i;
}
bin_to_q.resize(max_bin_number + 1);
for (int i = 0; i < max_bin_number + 1; i++)
bin_to_q[i] = static_cast<float>(q_spacing * (i + 0.5) + low_q);
solid_angle_corr.resize(max_bin_number + 1);
for (int i = 0; i < max_bin_number + 1; i++)
solid_angle_corr[i] = 1.0f / CalcRadIntSolidAngleCorr(experiment, bin_to_q[i]);
}
uint16_t RadialIntegrationMappingFPGA::GetBinNumber() const {
return max_bin_number + 1;
}
const std::vector<uint16_t> &RadialIntegrationMappingFPGA::GetPixelToBinMapping() const {
return pixel_to_bin;
}
const std::vector<float> &RadialIntegrationMappingFPGA::GetBinToQ() const {
return bin_to_q;
}
const std::vector<float> &RadialIntegrationMappingFPGA::GetSolidAngleCorr() const {
return solid_angle_corr;
}
double RadialIntegrationMappingFPGA::QToBin(double q) const {
return std::min(static_cast<double>(max_bin_number), std::max(0.0, (q - low_q) / q_spacing));
}

25
image_analysis/RadialIntegrationMappingFPGA.h Normal file
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@@ -0,0 +1,25 @@
// Copyright (2019-2023) Paul Scherrer Institute
#ifndef JUNGFRAUJOCH_RADIALINTEGRATIONMAPPINGFPGA_H
#define JUNGFRAUJOCH_RADIALINTEGRATIONMAPPINGFPGA_H
#include <vector>
#include <cstdint>
#include "../common/DiffractionExperiment.h"
class RadialIntegrationMappingFPGA {
const double low_q, high_q, q_spacing;
std::vector<float> bin_to_q;
std::vector<float> solid_angle_corr;
std::vector<uint16_t> pixel_to_bin;
uint16_t max_bin_number;
public:
explicit RadialIntegrationMappingFPGA(const DiffractionExperiment& experiment, uint16_t data_stream);
[[nodiscard]] uint16_t GetBinNumber() const;
[[nodiscard]] const std::vector<uint16_t> &GetPixelToBinMapping() const;
[[nodiscard]] const std::vector<float> &GetBinToQ() const;
[[nodiscard]] const std::vector<float> &GetSolidAngleCorr() const;
[[nodiscard]] double QToBin(double q) const;
};
#endif //JUNGFRAUJOCH_RADIALINTEGRATIONMAPPINGFPGA_H

6
receiver/AcquisitionDevice.cpp
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@@ -13,6 +13,7 @@
#include "../common/JFJochException.h"
#include "AcquisitionDevice.h"
#include "../common/NetworkAddressConvert.h"
#include "../image_analysis/RadialIntegrationMappingFPGA.h"
void *mmap_acquisition_buffer(size_t size, int16_t numa_node) {
void *ret = mmap(nullptr, size, PROT_READ | PROT_WRITE, MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);
@@ -43,6 +44,11 @@ void AcquisitionDevice::PrepareAction(const DiffractionExperiment &experiment) {
throw(JFJochException(JFJochExceptionCategory::InputParameterAboveMax,
"Number of modules exceeds max possible for FPGA"));
if (experiment.GetDetectorMode() == DetectorMode::Conversion) {
RadialIntegrationMappingFPGA map(experiment, data_stream);
InitializeIntegrationMap(experiment, map.GetPixelToBinMapping());
}
counters.Reset(experiment, data_stream);
}

1
receiver/AcquisitionDevice.h
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@@ -105,6 +105,7 @@ public:
// Calibration
virtual void InitializeCalibration(const DiffractionExperiment &experiment, const JFCalibration &calib);
virtual void InitializeIntegrationMap(const DiffractionExperiment &experiment, const std::vector<uint16_t> &v);
void InitializeIntegrationMap(const DiffractionExperiment& experiment);
const AcquisitionCounters& Counters() const;
virtual void SetSpotFinderParameters(int16_t count_threshold, double snr_threshold) {};

55
tests/RadialIntegrationTest.cpp
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@@ -3,7 +3,7 @@
#include <catch2/catch.hpp>
#include "../image_analysis/RadialIntegrationProfile.h"
#include "../image_analysis/RadialIntegrationMapping.h"
#include "../image_analysis/RadialIntegrationMappingFPGA.h"
#include "../image_analysis/RadialIntegration.h"
TEST_CASE("RadialIntegrationMapping_Constructor","[RadialIntegration]") {
@@ -15,6 +15,15 @@ TEST_CASE("RadialIntegrationMapping_Constructor","[RadialIntegration]") {
REQUIRE_NOTHROW(radial = std::make_unique<RadialIntegrationMapping>(x));
}
TEST_CASE("RadialIntegrationMappingFPGA_Constructor","[RadialIntegration]") {
DiffractionExperiment x;
std::unique_ptr<RadialIntegrationMappingFPGA> radial;
x.QSpacingForRadialInt_recipA(0.1).LowQForRadialInt_recipA(0.1).HighQForRadialInt_recipA(5);
REQUIRE_NOTHROW(radial = std::make_unique<RadialIntegrationMappingFPGA>(x, 0));
}
TEST_CASE("RadialIntegrationMapping_Constructor_Mask","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
@@ -41,6 +50,14 @@ TEST_CASE("RadialIntegrationMapping_GetBinNumber","[RadialIntegration]") {
REQUIRE(mapping.GetBinNumber() == 39);
}
TEST_CASE("RadialIntegrationMappingFPGA_GetBinNumber","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
x.QSpacingForRadialInt_recipA(0.1).LowQForRadialInt_recipA(0.1).HighQForRadialInt_recipA(4);
RadialIntegrationMappingFPGA mapping(x, 0);
REQUIRE(mapping.GetBinNumber() == 39);
}
TEST_CASE("RadialIntegrationMapping_GetBinNumber_DetectorLimit","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
@@ -50,6 +67,15 @@ TEST_CASE("RadialIntegrationMapping_GetBinNumber_DetectorLimit","[RadialIntegrat
REQUIRE(mapping.GetBinNumber() < 80);
}
TEST_CASE("RadialIntegrationMappingFPGA_GetBinNumber_DetectorLimit","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
x.QSpacingForRadialInt_recipA(0.1).LowQForRadialInt_recipA(0.1).HighQForRadialInt_recipA(9.9);
RadialIntegrationMappingFPGA mapping(x, 0);
REQUIRE(mapping.GetBinNumber() < 80);
}
TEST_CASE("RadialIntegrationMapping_GetBinToQ","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
@@ -64,6 +90,20 @@ TEST_CASE("RadialIntegrationMapping_GetBinToQ","[RadialIntegration]") {
REQUIRE(bin_to_q[38] == Approx(3.95));
}
TEST_CASE("RadialIntegrationMappingFPGA_GetBinToQ","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
x.QSpacingForRadialInt_recipA(0.1).LowQForRadialInt_recipA(0.1).HighQForRadialInt_recipA(4);
RadialIntegrationMappingFPGA mapping(x, 0);
auto bin_to_q = mapping.GetBinToQ();
REQUIRE(bin_to_q[0] == Approx(0.15));
REQUIRE(bin_to_q[1] == Approx(0.25));
REQUIRE(bin_to_q[15] == Approx(1.65));
REQUIRE(bin_to_q[38] == Approx(3.95));
}
TEST_CASE("RadialIntegrationMapping_QToBin","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
@@ -77,6 +117,19 @@ TEST_CASE("RadialIntegrationMapping_QToBin","[RadialIntegration]") {
REQUIRE(mapping.QToBin(50.0) == Approx(38));
}
TEST_CASE("RadialIntegrationMappingFPGA_QToBin","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
x.QSpacingForRadialInt_recipA(0.1).LowQForRadialInt_recipA(0.1).HighQForRadialInt_recipA(4);
RadialIntegrationMappingFPGA mapping(x, 0);
REQUIRE(mapping.QToBin(0.0) == 0);
REQUIRE(std::floor(mapping.QToBin(0.200001)) == 1);
REQUIRE(mapping.QToBin(0.6) == Approx(5));
REQUIRE(mapping.QToBin(50.0) == Approx(38));
}
TEST_CASE("RadialIntegrationProfile","[RadialIntegration]") {
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);