added hit_analyse_v2 class. Currently produces and fits a fake data set.

This commit is contained in:
Blake Leverington 2023-09-12 16:26:47 +02:00
parent 417615709d
commit f80b78e293
6 changed files with 723 additions and 14 deletions

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@ -1,5 +1,6 @@
#include "eventbuilder.h"
#include "udpserver.h"
#include "hit_analyse_v2.h"
EventBuilder::EventBuilder(QObject *parent) : QObject(parent)
{
@ -10,6 +11,7 @@ EventBuilder::EventBuilder(QObject *parent) : QObject(parent)
connect(this, EventBuilder::sigStartTakingHistos, this, EventBuilder::onStartTakingHistos);
connect(this, EventBuilder::sigStopTakingHistos, this, EventBuilder::onStopTakingHistos);
moveToThread(&thread);
thread.start();
init();
@ -52,18 +54,57 @@ void EventBuilder::onNewData(DataReceiver* receiver)
}
//************ TODO ************
//Here we can do something more with the complete frame
// I probably want to find the position and focus with the linear regression algorithm, but first, just send data to the udpserver to test.
//currentFrame[dev_nr].sensor_data[ch]
//currentFrame is BufferData
// unsigned short* sensor_data;
//ToDo:
//1. Background subtraction.
frame_counter++;
while (frame_counter<10000){
for (unsigned int dev_nr = 0; dev_nr < nrReceivers; dev_nr++){
for (unsigned int ch = 0; ch < channelCounts[dev_nr]; ch++)
backgroundFrame[dev_nr].sensor_data[ch]+= currentFrame[dev_nr].sensor_data[ch];
}
}
if (frame_counter==10000){
for (unsigned int dev_nr = 0; dev_nr < nrReceivers; dev_nr++){
for (unsigned int ch = 0; ch < channelCounts[dev_nr]; ch++)
backgroundFrame[dev_nr].sensor_data[ch]/= 10000 ;
}
}
if (frame_counter>10000){
for (unsigned int dev_nr = 0; dev_nr < nrReceivers; dev_nr++){
for (unsigned int ch = 0; ch < channelCounts[dev_nr]; ch++)
currentFrame[dev_nr].sensor_data[ch]-=backgroundFrame[dev_nr].sensor_data[ch] ;
}
}
lastFrameMutex.lock();
if (newDataSemaphore.available() == 0)
newDataSemaphore.release(1);
lastFrame = currentFrame;
lastFrameMutex.unlock();
//histogram stuff
//histogram stuff
if (histogramSamplesToTake)
{
for (int dev_nr = 0; dev_nr < nrReceivers; dev_nr++)
for (int ch = 0; ch < channelCounts[dev_nr]; ch++)
histograms[baseAddresses[dev_nr] + ch].shoot(currentFrame[dev_nr].sensor_data[ch]);
histograms[baseAddresses[dev_nr] + ch].shoot(currentFrame[dev_nr].sensor_data[ch]);
if (histogramSamplesToTake != -1)
histogramSamplesToTake--;
@ -71,19 +112,13 @@ void EventBuilder::onNewData(DataReceiver* receiver)
emit sigHistoCompleted();
}
//log data
if (loggingData)
logDataToFile();
//log data
if (loggingData) logDataToFile();
HIT_ANALYSE_V2 hit_analyse_v2;//create the object
QString dataString = hit_analyse_v2.analyseBeamData(currentFrame);
//************ TODO ************
//Here we can do something more with the complete frame
// I probably want to find the position and focus with the linear regression algorithm, but first, just send data to the udpserver to test.
intensity+=1.0;
position+=0.1;
focus+=0.01;
// Call sendData method of the UDP server
QString dataString = QString::number(intensity) + ',' + QString::number(position) + ',' + QString::number(focus);
//QString dataString = QString::number(intensity) + ',' + QString::number(position) + ',' + QString::number(focus);
QByteArray data = dataString.toUtf8();
udpServer.sendData(data);
@ -252,6 +287,7 @@ void EventBuilder::addSource(DataReceiver* source)
receivers.append(source);
nrReceivers = receivers.length();
currentFrame.resize(nrReceivers);
backgroundFrame.resize(nrReceivers);
connect(source, DataReceiver::sigDataReady, this, EventBuilder::onNewData);
}

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@ -64,6 +64,8 @@ protected:
QVector<DataReceiver*> receivers;
QVector<BufferData> currentFrame;
QVector<BufferData> backgroundFrame;
QVector<BufferData> lastFrame;
QVector<Histogram> histograms;
@ -88,6 +90,7 @@ protected slots:
void onStartTakingHistos(int sample_count);
void onStopTakingHistos();
private:
long unsigned int frame_counter = 0;
double intensity = 0.0;
double position = 0.0;
double focus = 0.0;

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@ -15,6 +15,7 @@ TEMPLATE = app
SOURCES += main.cpp\
hit_analyse_v2.cpp \
mainwindow.cpp \
q_debugstream.cpp \
dialoglogsettings.cpp \
@ -45,6 +46,7 @@ HEADERS += mainwindow.h \
device.h \
dev_commands.h \
datareceiver.h \
hit_analyse_v2.h \
hw.h \
dialoghostip.h \
dialogtriggersettings.h \
@ -63,7 +65,8 @@ HEADERS += mainwindow.h \
dialogprofiler.h \
stepper.h \
dialogbeta.h \
udpserver.h
udpserver.h \
hitreader.h
FORMS += mainwindow.ui \
dialoglogsettings.ui \

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@ -0,0 +1,154 @@
#include "hit_analyse_v2.h"
#include <random>
HIT_ANALYSE_V2::HIT_ANALYSE_V2(QObject *parent) : QObject(parent)
{
}
QString HIT_ANALYSE_V2::analyseBeamData(QVector<BufferData> dataframe){
double position=0.1;
double focus=8;
double intensity=10000.0;
QString dataString;
const int vector_length = 300; // Replace with the actual length of your vectors
std::vector<double> signal_list(vector_length);
std::vector<double> channel_list(vector_length);
// Create a random number generator with a Gaussian distribution
std::random_device rd;
std::mt19937 gen(rd());
std::normal_distribution<double> dist(0.0, 17.0); // Mean of 0 and Sigma of 17
// Create a vector to store the generated values
std::vector<short int> result(vector_length);
// Fill the vector with random values
for (int i = 0; i < vector_length; ++i) {
result[i] = static_cast<short int>(dist(gen));
signal_list.push_back(result[i]);
channel_list.push_back(i);
}
//add a gaussian profile, focus is FWHM, position is random between 50 and 250
position = 50 + (rand() % (int)(250 - 50 + 1));
for (int i = 0; i < vector_length; ++i) {
signal_list[i] += intensity*exp(-4*log(2)*pow((channel_list[i]-position)/focus,2));
}
// Fill signal_list and channel_list with your data
double SumT = 0.0, SumS = 0.0, SumS2 = 0.0, SumST = 0.0, SumT2 = 0.0, SumY = 0.0, SumYS = 0.0, SumYT = 0.0;
double b_den = 0.0, b_num = 0.0, b = 0.0, p = 0.0, c = 0.0, SumYYP = 0.0, SumYYM = 0.0, MeanY = 0.0;
double S[vector_length];
double T[vector_length];
for (int k = 0; k < vector_length; k++) {
if (k == 0) {
S[k] = 0.0;
T[k] = 0.0;
} else {
S[k] = S[k - 1] + 0.5 * (signal_list[k] + signal_list[k - 1]) * (channel_list[k] - channel_list[k - 1]);
T[k] = T[k - 1] + 0.5 * (channel_list[k] * signal_list[k] + channel_list[k - 1] * signal_list[k - 1]) *
(channel_list[k] - channel_list[k - 1]);
}
SumS += S[k];
SumT += T[k];
SumY += signal_list[k];
SumS2 += S[k] * S[k];
SumST += S[k] * T[k];
SumT2 += T[k] * T[k];
SumYS += signal_list[k] * S[k];
SumYT += signal_list[k] * T[k];
MeanY += signal_list[k];
}
MeanY /= vector_length;
// Calculate M1 matrix elements
double M1_00 = SumT2;
double M1_01 = SumST;
double M1_02 = SumT;
double M1_10 = SumST;
double M1_11 = SumS2;
double M1_12 = SumS;
double M1_20 = SumT;
double M1_21 = SumS;
double M1_22 = vector_length;
// Calculate M2 vector elements
double M2_0 = SumYT;
double M2_1 = SumYS;
double M2_2 = SumY;
// Calculate the inverse of M1
double detM1 = M1_00 * (M1_11 * M1_22 - M1_12 * M1_21) -
M1_01 * (M1_10 * M1_22 - M1_12 * M1_20) +
M1_02 * (M1_10 * M1_21 - M1_11 * M1_20);
if (detM1 == 0.0) {
std::cerr << "M1 is not invertible." << std::endl;
//return 1;
}
double invM1_00 = (M1_11 * M1_22 - M1_12 * M1_21) / detM1;
double invM1_01 = (M1_02 * M1_21 - M1_01 * M1_22) / detM1;
double invM1_02 = (M1_01 * M1_12 - M1_02 * M1_11) / detM1;
double invM1_10 = (M1_12 * M1_20 - M1_10 * M1_22) / detM1;
double invM1_11 = (M1_00 * M1_22 - M1_02 * M1_20) / detM1;
double invM1_12 = (M1_02 * M1_10 - M1_00 * M1_12) / detM1;
double invM1_20 = (M1_10 * M1_21 - M1_11 * M1_20) / detM1;
double invM1_21 = (M1_01 * M1_20 - M1_00 * M1_21) / detM1;
double invM1_22 = (M1_00 * M1_11 - M1_01 * M1_10) / detM1;
// Calculate ABC vector
double ABC_0 = invM1_00 * M2_0 + invM1_01 * M2_1 + invM1_02 * M2_2;
double ABC_1 = invM1_10 * M2_0 + invM1_11 * M2_1 + invM1_12 * M2_2;
double ABC_2 = invM1_20 * M2_0 + invM1_21 * M2_1 + invM1_22 * M2_2;
// Calculate b, p, and c
p = -ABC_0 / 2.0;
c = -ABC_1 / ABC_0;
for (int k = 0; k < vector_length; k++) {
double exp_term = exp(-p * (channel_list[k] - c) * (channel_list[k] - c));
b_num += exp_term * signal_list[k];
b_den += exp_term;
}
b = b_num / b_den;
for (int k = 0; k < vector_length; k++) {
double y_pred = b * exp(-p * (channel_list[k] - c) * (channel_list[k] - c));
SumYYM += (signal_list[k] - MeanY) * (signal_list[k] - MeanY);
SumYYP += (y_pred - MeanY) * (y_pred - MeanY);
}
double R_squared = SumYYP / SumYYM;
//std::cout << "R-squared = " << R_squared << endl;
position = -ABC_1/ ABC_0;
//sigma = sqrt(1.0 / (2.0 * ABC_0));
focus = 2.3548/sqrt(2*p);
intensity = b;
dataString += QString::number(intensity) + ',' + QString::number(position) + ',' + QString::number(focus)
+ ',' + QString::number(R_squared);
return dataString;
}
HIT_ANALYSE_V2::~HIT_ANALYSE_V2()
{
}

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@ -0,0 +1,72 @@
#ifndef HIT_ANALYSE_V2_H
#define HIT_ANALYSE_V2_H
#include <string>
#include <stdio.h>
#include <iostream>
#include <numeric>
#include <vector>
#include <algorithm> // std::count
#include <utility>
#include <math.h>
#include <fstream>
#include <iomanip> // std::setprecision
#include <QObject>
#include <QUdpSocket>
#include <complex.h>
#include <stdlib.h>
#include "datareceiver.h"
//#include <gsl/gsl_errno.h>
//#include <gsl/gsl_fft_complex.h>
//#include <gsl/gsl_sort.h>
//#include <gsl/gsl_statistics.h>
class HIT_ANALYSE_V2 : public QObject
{
Q_OBJECT
public:
explicit HIT_ANALYSE_V2(QObject *parent = nullptr);
~HIT_ANALYSE_V2();
private:
struct beamRecon {
double Position;
double Focus;
double Peak;
double Rsqr;
double Skew;
double Kurtosis;
double Sum;
int n_channels;
};
struct bpm_frame_v2 {
double channel_amp[320];
double channel_position[320];
double avg_position;
double avg_width;
double integratedsignalamp;
double maxchannel_amp;
int maxchannel;
int nrChannels;
int board_number;
int sma_state;
};
public slots:
QString analyseBeamData(QVector<BufferData> dataframe);
// void processPendingDatagrams();
};
class Channel{
public:
double amplitude;;
double position;
int chnumber;
int last_neighbour;
int next_neighbour;
};
#endif // HIT_ANALYSE_V2_H

441
hit2023v2/hitreader.h Normal file
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@ -0,0 +1,441 @@
//This is an object interface for reading HIT data files
//See HIT documentation for details and examples.
/*
THIS DOESN'T WORK!
.L hitreader.c
Hitdata data;
data.read(my_file.da2); //to load whole file at once forget it! See below.
data.read(my_file.da2,1000,100,10) //to read 100 frames starting from frame 1000 and incrementing by 10 (i.e. frame 1000, 1010, 1020, ... 1990 will be read)
//Reading 10 000 frames is reasonable. Reading 100 000 frames made my VM beg for memory.
data.nrFrames //to see how many frames you have
data.frames[0].nrBoards //to see how many boards you had in the system
data.frames[0].boards[0].nrChannels //to see how many channels you have in board 0
data.frames[10].boards[0].data[100] //get signal value for frame 10, board 0, channel 100
data.frames[10].boards[0].syncframe.local_ctr //get the local synchro counter for frame 10, board 0
//same for .global_ctr, .sma_state, .dummy, .device_nr, .data_ok
*/
//*********************** Helper *************************
#include <fstream>
#include <iostream>
using namespace std;
//#define debug(str) std::cout << "HIT DEBUG: " << str << endl;
#define debug(str)
//*********************** Syncframe *************************
class Syncframe
{
public:
Syncframe()
{
debug("Syncframe()");
local_ctr = global_ctr = 0;
sma_state = dummy = 0;
device_nr = -1;
data_ok = 0;
};
~Syncframe()
{
debug("~Syncframe()");
};
int sizeInFile()
{
return 16;
};
int read(std::ifstream* file)
{
char buffer[16];
file->read(buffer,16);
if (file->fail())
return 0;
local_ctr = *(unsigned short*)(buffer+0);
global_ctr = *(unsigned short*)(buffer+2);
sma_state = *(unsigned short*)(buffer+4);
dummy = *(unsigned short*)(buffer+6);
device_nr = *(int*)(buffer+8);
data_ok = *(int*)(buffer+12);
// std::cout << "Syncframe:" << local_ctr << " " << global_ctr << " " << sma_state << " " << dummy << " " << device_nr << " " << data_ok << std::endl;
return 1;
};
unsigned short local_ctr;
unsigned short global_ctr;
unsigned short sma_state;
unsigned short dummy;
int device_nr;
unsigned int data_ok;
};
//*********************** Sensorframe *************************
class Boardframe
{
public:
Boardframe(int nr_channels = 0)
{
debug("Boardframe()");
data = NULL;
resize (nr_channels);
};
Boardframe(const Boardframe& in)
{
debug("Boardframe(Boardframe&)");
data = NULL;
resize(in.nrChannels);
for (int i = 0; i < nrChannels; i++)
data[i] = in.data[i];
syncframe = in.syncframe;
};
Boardframe& operator=(const Boardframe& in)
{
debug("Boardframe::operator==");
resize(in.nrChannels);//creates an array called data of length nrChannels
for (int i = 0; i < nrChannels; i++)
data[i] = in.data[i];
syncframe = in.syncframe;
return *this;
};
~Boardframe()
{
debug("~Boardframe()");
if (data)
delete[] data;
};
void resize(int nr_channels)
{
if (data)
delete[] data;
nrChannels = nr_channels;
if (nrChannels)
data = new unsigned short[nrChannels];
else
data = NULL;
};
int sizeInFile()
{
// std::cout << "boardframe.sizeInFile() = " << syncframe.sizeInFile() + nrChannels*2 << std::endl;
return syncframe.sizeInFile() + nrChannels*2;
};
int read(std::ifstream* file)
{
if (syncframe.read(file) == 0)//get the syncframe before the board data
return 0;
//I must be already resized at this point!
file->read((char*)data,2*nrChannels);
if (file->fail())
return 0;
// std::cout<< "data[" << nrChannels << "]: ";
// for (int i = 0;i<nrChannels;i++) std::cout << data[i] << " ";
// std::cout << std::endl;
return 1;
};
unsigned short& operator[] (int index)
{
return data[index];
};
Syncframe syncframe;
int nrChannels;
unsigned short* data;
};
//*********************** Fullframe *************************
class Fullframe
{
public:
Fullframe(int nr_boards = 0)
{
debug("Fullframe()");
boards = NULL;
resize(nr_boards);
};
Fullframe(const Fullframe& in)
{
debug("Fullframe(Fullframe&)");
boards = NULL;
resize(in.nrBoards);
for (int i = 0; i < nrBoards; i++)
boards[i] = in.boards[i];
};
Fullframe& operator=(const Fullframe& in)
{
debug("Fullframe::operator==");
resize(in.nrBoards);
for (int i = 0; i < nrBoards; i++)
boards[i] = in.boards[i];
return *this;
};
~Fullframe()
{
debug("~Fullframe()");
if (boards)
delete[] boards;
};
void resize (int nr_boards)
{
if (boards)
delete[] boards;
nrBoards = nr_boards;
if (nrBoards)
boards = new Boardframe[nrBoards];
else
boards = NULL;
}
int sizeInFile()
{
if (boards){
// std::cout << "Fullframe.sizeInFile() = " << 2 + nrBoards*2 + nrBoards * boards[0].sizeInFile() << std::endl;
// return 2 + nrBoards*2 + nrBoards * boards[0].sizeInFile();
//// boards[0].sizeInFile() returns 656 for every board...
return 2 + 4*2 + (16 + 320 * 2) + (16 + 128*2)*3; //1482
}
else
return 0; //no boards, makes no sense...
};
int read(std::ifstream* file)
{
//Read number of boards
unsigned short nr_boards;
file->read((char*)&nr_boards,2);
if(file->fail()){
std::cerr << "File read failed." << std::endl;
return 0;
}
if (nr_boards!=4){
std::cerr << "Unrealistic number(!=) of boards to be read:"<< nr_boards << std::endl;
std::cerr << "Will try to resync frame." << std::endl;
for (int j = 0;j<741;j++){
file->read((char*)&nr_boards,2);
if (nr_boards==4) break;
}
if ( nr_boards!=4){
std::cerr << "Resync failed." << std::endl;
return 0;
}
}
//std::cout << " nr_boards: " << nr_boards << std::endl;
//Read channel counts
unsigned short* channel_counts = new unsigned short[nr_boards];
file->read((char*)channel_counts,nr_boards*2);
if (file->fail())
{
delete[] channel_counts;
return 0;
}
//Read board frames
resize(nr_boards);
for (int board_nr = 0; board_nr < nr_boards; board_nr++)
{
// std::cout << " channel_counts[" << board_nr << "]: "<< channel_counts[board_nr] << std::endl;
boards[board_nr].resize(channel_counts[board_nr]);
if (boards[board_nr].read(file) == 0)//read the board
{
delete[] channel_counts;
return 0;
}
}
delete[] channel_counts;
return 1;
};
int nrChannels()
{
int result = 0;
for (int board_nr = 0; board_nr < nrBoards; board_nr++)
result += boards[board_nr].nrChannels;
return result;
};
unsigned short& operator[] (int index)
{
for (int board_nr = 0; board_nr < nrBoards; board_nr++)
{
if (index >= boards[board_nr].nrChannels)
index -= boards[board_nr].nrChannels;
else
return boards[board_nr][index];
}
std::cerr << " ### Fullframe::operator[]: index out of range!" << std::endl;
// return (*NULL); //this will cause crash (intended).
return boards[nrBoards][index];
};
int nrBoards;
Boardframe* boards;
};
//*********************** Hitdata *************************
class Hitdata
{
public:
Hitdata(int nr_frames = 0)
{
frames = NULL;
resize(nr_frames);
};
Hitdata(const Hitdata& in)
{
frames = NULL;
resize(in.nrFrames);
for (int i = 0; i < nrFrames; i++)
frames[i] = in.frames[i];
};
Hitdata& operator=(const Hitdata& in)
{
resize(in.nrFrames);
for (int i = 0; i < nrFrames; i++)
frames[i] = in.frames[i];
return *this;
};
~Hitdata()
{
if (nrFrames)
delete[] frames;
};
void resize (int nr_frames)
{
if (nrFrames)
delete[] frames;
nrFrames = nr_frames;
if (nrFrames)
frames = new Fullframe[nrFrames];
else
frames = NULL;
};
//Read data from a given file.
//first_frame is the number of first frame to be read
//nr_frames is the maximum number of frames to be read
//-1 to read all of them
//increment allows you reading once every nth sample
//Return number of frames read or 0 in case of failure
int readFile(char* filename, int first_frame = 1, int nr_frames = -1, int increment = 1)
{
std::ifstream file;
//Open the file
file.open(filename, ios_base::in | ios_base::binary);
if (!file.is_open())
{
std::cerr << " ### Hitdata: File could not be open!" << std::endl;
return 0; //file could not be opened
}
//Read first record to find board configuration
Fullframe sampleframe;
if (sampleframe.read(&file) == 0)
{
std::cerr << " ### Hitdata: First frame could not be read!" << std::endl;
file.close();
return 0;
}
else {
std::cout << "Sample frame size (bytes): " << sampleframe.sizeInFile() << std::endl;
}
//Check file size
file.seekg(0, std::ios::beg);
std::streamsize fsize = file.tellg();
file.seekg(0, std::ios::end);
fsize = file.tellg() - fsize;
//Determine real frames to read
unsigned int max_frames = fsize / sampleframe.sizeInFile();
if ((max_frames == -1) || (max_frames < nr_frames))
nr_frames = max_frames;
std::cout << " Hitdata: Nr frames to be read: " << nr_frames << std::endl;
//Read!
// resize(nr_frames); //make an array of Fullframes called frames of size nr_frames
file.seekg(first_frame * sampleframe.sizeInFile(), std::ios::beg);
for (int frame_nr = first_frame; frame_nr < nr_frames; frame_nr++)
{
if ((frame_nr%10000) == 0)
std::cout << " Frame " << frame_nr << std::endl;
file.seekg((frame_nr*increment) * sampleframe.sizeInFile() , std::ios::beg);
if (file.eof()) {
std::cerr<< "end of file reached." << std::endl;
return frame_nr;
}
if ( sampleframe.read(&file) == 0) //read the next frame
{
std::cerr << " ### Hitdata: Frame " << frame_nr << " could not be read!" << std::endl;
file.close(); //read error, finish!
// frames = frame_nr; //Kinky! We decrease nr_frames, but the actual array size remains unchanged!
///???? I don't know what the above line does.
return frame_nr;
}
// std::cout << frames[frame_nr].nrBoards << std::endl;
}
//Finished
file.close();
return nr_frames;
};
Fullframe& operator[] (int index)
{
if (index < nrFrames)
return frames[index];
else
{
std::cerr << " ### Hitdata::operator[]: index out of range!" << std::endl;
// return (*NULL); //this will cause crash (intended).
return frames[index];
}
};
int nrFrames;
Fullframe* frames;
};