Beam hardening correction: Bath example
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Introduction
This example using the config file named config.txt to configure steps of the process. File contents is like this:
o, First: line type: o - comment, r - referrence plate, m - measuring
o, Ref. cfg. line: r, thickness [mm], acqTime [s], num of expositions, output files: d data / p picture / b both / n none, name
r, 0, 0.005, 200, d, dir_beam
r, 1, 0.006, 200, d, ref_1
r, 2, 0.010, 200, d, ref_2
r, 3, 0.015, 200, d, ref_3
o, Measuring cfg. line: m, acqTime [s], num of expositions, bad px setting: d device / b BH system, output files: d data / p picture / b both / n none, name
m, 0.005, 200, d, b, test1
m, 0.005, 200, d, b, test2
m, 0.01, 200, b, b, test3
m, 0.02, 200, b, b, test4The example program read the line, display it in the console, will ask if it should do it and wait for user response. If yes, program acquire required number of frames, view simple histogram in the console, do the processing and save images, if reqired.
This example is using many auxiliary functions. Complete code is in the example project named MiniPixTpx3-Thickness-bath. To get usable acquisition times do a experimental exposures in the Pixet program, or get them using a second sample project named MiniPixTpx3-Thickness-auto that has auto-tuning and image preview in the console.
Code
/**
* Copyright (C) 2021 ADVACAM
* @author Pavel Hudecek <pavel.hudecek@advacam.com>
*
* Example of thickness measuring with beam hardening compensation feature
* B - Bath version
*/
/* Used API functions:
pxcGetLastError
pxcInitialize
pxcGetDevicesCount
pxcGetDeviceName
pxcGetDeviceChipID
pxcSetTimepix3Mode
pxcMeasureSingleFrameTpx3
pxcGetMeasuredFrameTpx3
pxcMeasureMultipleFrames
pxcMeasureMultipleFramesWithCallback
pxcRegisterAcqEvent
pxcMeasureContinuousTest
pxcAbortMeasurement
pxcAddBHMask
pxcBHMaskCount
pxcRemoveBHMask
pxcApplyBHCorrection
pxcGetDeviceBadPixelMatrix
pxcGetBHBadPixelMatrix
pxcInterpolateBadPixels
pxcGetDeviceAndBHBadPixelMatrix
requires: pxcapi.h, pxcore.dll, minipix.dll, pixet.ini, link with pxcore.lib
*/
#include "pxcapi.h"
#include <cstring>
#include <iostream>
#include <conio.h>
#include <thread>
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <sstream>
//#include <vector>
using namespace std;
// wait for user choice from 2 to 3 keys (key3=0 or key4=0 -> not used)
// key1/key2/key3 is lower case, keyboard input is independent ===================================
char choiceKey(char key1, char * text1, char key2, char * text2, char key3=0, char * text3="", char key4=0, char * text4="") {
char ch;
while(1) {
ch = _getch();
if (ch<'a' && ch>='A' && ch<='Z') ch += 'z'-'Z'; // convert to lower case
if (ch==key1) {
if (text1[0]!=0) printf("%s\n", text1);
break;
} else if (ch==key2) {
if (text2[0]!=0) printf("%s\n", text2);
break;
} else if (key3!=0) if (ch==key3) {
if (text3[0]!=0) printf("%s\n", text3);
break;
} else if (key4!=0) if (ch==key4) {
if (text4[0]!=0) printf("%s\n", text4);
break;
}
}
return ch;
}
#define ERRMSG_BUFF_SIZE 512
#define ENTER_ON true
#define ENTER_OFF false
// primary use to show function name, return code, last error message and optional enter
void printErrors(const char* fName, int rc, bool enter) { // ===================================
char errorMsg[ERRMSG_BUFF_SIZE];
pxcGetLastError(errorMsg, ERRMSG_BUFF_SIZE);
if (errorMsg[0]>0) {
printf("%s %d err: %s", fName, rc, errorMsg);
} else {
printf("%s %d err: ---", fName, rc);
}
if (enter) printf("\n");
}
#define ABORT_only true
#define ABORT_ask false
// if rc!=0 printError and return true or ask the user for quit (return true for quit)
bool errorCheck(char * fName, int rc, bool abortOnly) { // =====================================
if (rc!=0) {
printErrors(fName, rc, ENTER_ON);
printf("Press A to abort or C to continue:\n");
if (abortOnly==ABORT_ask) {
if (choiceKey('a', "Choice: Abort", 'c', "Choice: Continue")=='c') return false;
}
return true;
}
return false;
}
#define CHT_Si 0
#define CHT_CdTe 1
char chipType = CHT_Si;
const unsigned CHIP_xRes = 256;
const unsigned CHIP_yRes = 256;
const unsigned CHIP_pixels = CHIP_xRes * CHIP_yRes;
unsigned fileIdx=0; // index of saved file
double saveTmpD[CHIP_pixels]; // temp for convert in saveTo.. overload
// Save image to file. Fname add info: exposition, min, max, limit (frames*1023), chip
// Data auto-ranged to min-max
// Filename is automatically incremented, but only in the session. Old files can be overwritten.
void saveToBMP(double *frame, char *info, double expos, unsigned limit=0) { // ============================
const unsigned HEAD_end = 54;
static unsigned char fTmp[HEAD_end + CHIP_pixels * 3] = { // image file temp
'B', 'M', 54, 0, 3, 0, 0, 0, 0, 0, 54, 0, 0, 0, 40, 0,
0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 24, 0, 0, 0,
0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
}; // header of 24b BMP file, size 256x256
// 2-6 file size, 10-14 data offset, 14-17 DIB head size, 18-21 width, 22-25 height, 28/29 bits per px, 38-41 x pix/m, 42-45 y pix/m
char fName[150];
char chip[]="CdTe";
FILE *imageFile;
unsigned n;
printf("Saving... ");
double min=4000000000.0, max=0.0;
for (n=0; n<CHIP_pixels; n++) {
if (frame[n]<min) min = frame[n];
if (frame[n]>max) max = frame[n];
}
for (n=0; n<CHIP_pixels; n++) { // convert the data -----------------
fTmp[HEAD_end+n*3+0] = (unsigned char)((frame[n]-min) * 255.0 / (max-min));
fTmp[HEAD_end+n*3+1] = (unsigned char)((frame[n]-min) * 255.0 / (max-min));
fTmp[HEAD_end+n*3+2] = (unsigned char)((frame[n]-min) * 255.0 / (max-min));
}
if (++fileIdx>999) fileIdx=0;
if (chipType==CHT_Si) strcpy_s(chip, 5, "Si");
sprintf_s(fName, 150, "img-%03u-%s exp_%1.2e_s min_%1.2e max_%1.2e lim_%u %s.bmp", fileIdx, info, expos, min, max, limit, chip);
if (fopen_s(&imageFile, fName, "wb")!=0) {
printf("ERROR: Cannot open image file");
return;
}
for (n = 0; n < HEAD_end + CHIP_pixels*3; n++) {
fprintf(imageFile, "%c", fTmp[n]);
}
fclose(imageFile);
printf("Saved file: %s\n", fName);
}
void saveToBMP(unsigned *frame, char *info, double expos, unsigned limit=0) { // ==========================
for (unsigned n=0; n<CHIP_pixels; n++) {
saveTmpD[n] = (double)frame[n];
}
saveToBMP(saveTmpD, info, expos, limit);
}
void saveToTXT(double *frame, char *info, double expos, unsigned limit=0) { // ============================
char fName[150];
char chip[]="CdTe";
FILE *imageFile;
unsigned n;
printf("Saving... ");
double min=4000000000.0, max=0.0;
for (n=0; n<CHIP_pixels; n++) {
if (frame[n]<min) min = frame[n];
if (frame[n]>max) max = frame[n];
}
if (++fileIdx>999) fileIdx=0;
if (chipType==CHT_Si) strcpy_s(chip, 5, "Si");
sprintf_s(fName, 150, "img-%03u-%s exp_%1.2e_s min_%1.2e max_%1.2e lim_%u %s.txt", fileIdx, info, expos, min, max, limit, chip);
if (fopen_s(&imageFile, fName, "wt")!=0) {
printf("ERROR: Cannot open image file");
return;
}
for (n = 0; n < CHIP_pixels; n++) {
fprintf(imageFile, "%f", frame[n]);
if (n < CHIP_pixels-1 && !(n % 256)) fprintf(imageFile, "\n");
else fprintf(imageFile, ", ");
}
fclose(imageFile);
printf("Saved file: %s\n", fName);
}
void saveToTXT(unsigned *frame, char *info, double expos, unsigned limit=0) { // ============================
for (unsigned n=0; n<CHIP_pixels; n++) {
saveTmpD[n] = (double)frame[n];
}
saveToTXT(saveTmpD, info, expos, limit);
}
// show 1 line histogram of single frame
void showHistogram(unsigned *data) { // ==========================================================
unsigned hist[100+5];
unsigned n, max, hDiv, avg;
for (n=0; n<100; n++) hist[n]=0;
for (n=0, max=0; n<CHIP_pixels; n++) if (data[n]>max) max=data[n];
hDiv = max/100;
for (n=0; n<CHIP_pixels; n++) hist[data[n]/hDiv]++;
for (n=0, max=0, avg=0; n<100; n++) {
if (hist[n]>max) max=hist[n];
avg += hist[n];
}
avg /= 100;
printf("Histogram: 0|");
for (n=0; n<100; n++) {
if (hist[n]>=avg*10) {
printf("#");
} else if (hist[n]>=avg*2) {
printf("*");
} else if (hist[n]>=avg/5) {
putchar('0' + (hist[n] * 5) / avg);
} else if (hist[n]>=avg/10) {
printf(".");
} else {
printf("_");
}
}
printf("|max\n");
}
// integrate multiple acqs to "data" array
int multiAcq(double frameTime, unsigned frameCount, unsigned *data) { // ================================
static unsigned short frameTotEvent[CHIP_pixels];
static double tmp[CHIP_pixels];
int rc; // return codes
unsigned fn, pn; // frame number, pixel number
unsigned size = CHIP_pixels; // buffer/chip pixel count, input/output pxcMeasureSingleFrameTpx3
cout << "multiAcq time=" << frameTime << " cnt=" << frameCount << ": ";
for (pn=0; pn<CHIP_pixels; pn++) data[pn]=0;
for (fn=0; fn<frameCount; fn++) {
cout << ".";
rc = pxcMeasureSingleFrameTpx3(0, frameTime, tmp, frameTotEvent, &size, PXC_TRG_NO);
if (rc!=0) return rc;
for (pn=0; pn<CHIP_pixels; pn++) data[pn] += (unsigned)frameTotEvent[pn];
}
cout << endl;
showHistogram(data);
return 0;
}
inline string trim(string& str) { // =====================================================================
str.erase(0, str.find_first_not_of(' ')); //prefixing spaces
str.erase(str.find_last_not_of(' ')+1); //surfixing spaces
return str;
}
int measureThicknessBH() { // ============================================================================
int rc; // return codes
unsigned frameTmp[CHIP_pixels]; // measured data
double frameOut[CHIP_pixels]; // BH corrected output data
unsigned char badPixels[CHIP_pixels];// combined "bad" pixels from pxcGetDeviceAndBHBadPixelMatrix
double frameTime; // frame acquisition time
double refThick; // thickness of ref. plate
char fileSet; // files setting: d - data, p - picture, b - both, n - none
char bpSet; // bad px setting: c - chip, b - BH system
string name; // line name/comment and used in output filenames
unsigned size = CHIP_pixels; // buffer/chip pixel count, input/output pxcMeasureSingleFrameTpx3
string line, valStr; // for config lines decoding
fstream cfgFile("config.txt", ios::in);
unsigned n, lineCnt;
char fileOutName[20], fileOutName2[20], fileOutName3[20]; // output filenames
rc = pxcSetTimepix3Mode(0, PXC_TPX3_OPM_EVENT_ITOT); // set mode on device 0
if (errorCheck("pxcSetTimepix3Mode", rc, ABORT_ask)) return -1;
lineCnt=1;
while (getline(cfgFile, line, '\n')) {
cout << "L " << lineCnt++ << " > " << line << endl;
stringstream linestream(line);
getline(linestream, valStr, ',');
switch (valStr.at(0)) { // -------------------------------------------------------
case 'o': // comment
break;
case 'r': // reference
case 'm': // measuring
cout << "- Prepare this step and pres Y to do this, or press N to No: ";
if (choiceKey('y', "Yes", 'n', "No")=='n') continue;
}
switch (valStr.at(0)) { // -------------------------------------------------------
case 'o': // comment
break;
case 'r': // reference -----------------------------------------------
getline(linestream, valStr, ','); // ref thick
refThick = stof(valStr);
getline(linestream, valStr, ','); // acq time
frameTime = stof(valStr);
getline(linestream, valStr, ','); // num of expositions
n = stoi(valStr);
multiAcq(frameTime, n, frameTmp); // measure
getline(linestream, valStr, ','); // file saving settings
fileSet = trim(valStr).at(0);
//cout << "fs >" << valStr << "<" << endl;
getline(linestream, name, ','); // name of the step and files
name = trim(name);
if (fileSet!='n') {
cout << "save " << name << " set=" << fileSet << endl;
strcpy_s(fileOutName, 20, name.c_str());
}
if (fileSet=='d') { // data file
saveToTXT(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
} else if (fileSet=='p') { // picture file
saveToBMP(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
} else if (fileSet=='b') { // both files
saveToBMP(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
saveToTXT(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
}
rc = pxcAddBHMask(frameTmp, CHIP_pixels, frameTime*(double)n, refThick);
if (errorCheck("pxcAddBHMask", rc, ABORT_ask)) return -1;
break;
case 'm': // measuring ---------------------------------------------------
getline(linestream, valStr, ','); // acq time
frameTime = stof(valStr);
getline(linestream, valStr, ','); // num of expositions
n = stoi(valStr);
multiAcq(frameTime, n, frameTmp); // measure
getline(linestream, valStr, ','); // bad px settings
bpSet = trim(valStr).at(0);
getline(linestream, valStr, ','); // file saving settings
fileSet = trim(valStr).at(0);
getline(linestream, name, ','); // name of the step and files
name = trim(name);
if (fileSet!='n') {
cout << "save " << name << " set=" << fileSet << endl;
strcpy_s(fileOutName, 20, (name + "-raw").c_str());
strcpy_s(fileOutName2, 20, (name + "-bhc").c_str());
strcpy_s(fileOutName3, 20, (name + "-bpc").c_str());
}
if (fileSet=='d') { // data file raw
saveToTXT(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
} else if (fileSet=='p') { // picture file raw
saveToBMP(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
} else if (fileSet=='b') { // both files raw
saveToBMP(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
saveToTXT(frameTmp, fileOutName, frameTime*(double)n, 1023*n);
}
rc = pxcApplyBHCorrection(frameTmp, CHIP_pixels, frameTime*(double)n, frameOut);
if (errorCheck("pxcApplyBHCorrection", rc, ABORT_ask)) return -1;
if (fileSet=='d') { // data file BH corrected
saveToTXT(frameOut, fileOutName2, frameTime*(double)n, 1023*n);
} else if (fileSet=='p') { // picture file BH corrected
saveToBMP(frameOut, fileOutName2, frameTime*(double)n, 1023*n);
} else if (fileSet=='b') { // both files BH corrected
saveToBMP(frameOut, fileOutName2, frameTime*(double)n, 1023*n);
saveToTXT(frameOut, fileOutName2, frameTime*(double)n, 1023*n);
}
if (bpSet=='d') { // bad px setting: d - device, b - device + BH system
rc = pxcGetDeviceBadPixelMatrix(0, badPixels, CHIP_pixels);
if (errorCheck("pxcGetDeviceBadPixelMatrix", rc, ABORT_ask)) return -1;
} else {
rc = pxcGetDeviceAndBHBadPixelMatrix(0, badPixels, CHIP_pixels);
if (errorCheck("pxcGetDeviceAndBHBadPixelMatrix", rc, ABORT_ask)) return -1;
}
//for (n=0; n<CHIP_pixels; n++) badPixels[n] = (unsigned char)frameTmp[n];
rc = pxcInterpolateBadPixels(badPixels, frameOut, 256, 256);
if (errorCheck("pxcInterpolateBadPixels", rc, ABORT_ask)) return -1;
if (fileSet=='d') { // data file BH+BP corrected
saveToTXT(frameOut, fileOutName3, frameTime*(double)n, 1023*n);
} else if (fileSet=='p') { // picture file BH+BP corrected
saveToBMP(frameOut, fileOutName3, frameTime*(double)n, 1023*n);
} else if (fileSet=='b') { // both files BH+BP corrected
saveToBMP(frameOut, fileOutName3, frameTime*(double)n, 1023*n);
saveToTXT(frameOut, fileOutName3, frameTime*(double)n, 1023*n);
}
break;
default:
cout << "Unknown line type: " << valStr << endl;
}
}
return 0;
}
int main (int argc, char const* argv[]) { // ###################################################
// Initialize Pixet
int rc = pxcInitialize();
if (rc) {
printf("Could not initialize Pixet:\n");
printErrors("pxcInitialize", rc, ENTER_ON);
return -1;
}
int connectedDevicesCount = pxcGetDevicesCount();
printf("Connected devices: %d\n", connectedDevicesCount);
if (connectedDevicesCount == 0) return pxcExit();
for (unsigned devIdx = 0; (signed)devIdx < connectedDevicesCount; devIdx++){
char deviceName[256];
memset(deviceName, 0, 256);
pxcGetDeviceName(devIdx, deviceName, 256);
char chipID[256];
memset(chipID, 0, 256);
pxcGetDeviceChipID(devIdx, 0, chipID, 256);
printf("Device %d: Name %s, (first ChipID: %s), ", devIdx, deviceName, chipID);
double bias;
rc = pxcGetBias(devIdx, &bias);
if (bias<0.0) {
if (devIdx==0) chipType = CHT_CdTe;
printf("Chip material detected: CdTe\n");
} else if (bias==0.0) {
if (devIdx==0) chipType = CHT_CdTe;
printf("Chip material not detected!\n");
} else {
if (devIdx==0) chipType = CHT_Si;
printf("Chip material detected: Si\n");
}
}
printf("====================================================================================================\n");
measureThicknessBH();
printf("Exiting...\n");
return pxcExit(); // Exit Pixet core
}