Keymer Lab in silico rasperry pi and ocean optics

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This project uses a Ocean optics spectrometer and a raspberry pi to measure continuously a culture of e.coli growing in a spectrometry cuvette. It is written in C and uses the open source seabreeze API and a raspberry pi 2 running NOOBS. It also uses the gnuplot_i C library to plot the results using a gnuplot session from a C programm.

Testing your installation

Before running place yourself in the /seabreeze-x.x.x/SeaBreeze/ directory and run the command: <syntaxhighlight lang="powershell" line="1" > $ export LD_LIBRARY_PATH="$PWD/lib" </syntaxhighlight>

Once that is done go in sample-code/c and to test your device run demo-averaging.c . If it your device is connected and up and running it should ask you for integration time and number of scans to average. Once those are entered the program will run for a bit and display a table with wavelengths and counts.

Measuring continuously and plotting in realtime

To run the continuous measurement place the File:Demo-continuous measurement.c file in sample-code/c . Then also place the gnuplot_i.c and gnuplot_i.h in sample-code/c . You the need to modify the makefile of sample-code/c as such: <syntaxhighlight lang="make" line="1" > SEABREEZE = ../..

APPS = seabreeze-util $(basename $(wildcard demo-*.c)) OBJS = $(addsuffix .o,$(APPS)) UTIL = util.o GNUPLOT = gnuplot_i.o all: $(APPS)

include $(SEABREEZE)/common.mk

$(APPS) : $(OBJS) $(UTIL) $(GNUPLOT) @echo linking $@ @$(CC) -o $@ $@.o $(UTIL) $(GNUPLOT) -lseabreeze $(LFLAGS_APP) -lpthread </syntaxhighlight>

This allows us to link the gnuplot_i library to the compilation of the files in sample-code/c

The C programm that allows us to plot and save in a csv file in real time

This code uses part of the demo-averaging.c file that can be found in the open-source seabreeze API of Ocean Optics. It is found under sample-code/c <syntaxhighlight lang="c" line="1" >

1. include <stdio.h>
2. include <stdlib.h>
3. include <string.h>
4. include <pthread.h>
5. include <time.h>
6. include <unistd.h>
7. include <sys/time.h>
8. include <errno.h>
9. include "api/SeaBreezeWrapper.h"
10. include "util.h"
11. include "gnuplot_i.h"

1. ifdef _WIN32
2. include <windows.h>
3. endif

1. define MAX_LABEL_SIZE 15

double * shiftarray(double *old_array, double new_value, int size_array); double * blank(double *stor_array, double value, int size_array);

int main(int argc, char **argv) {

   	int error = 0;
   	logger_header("Output from %s", argv[0]);

   ////////////////////////////////////////////////////////////////////////////
   // open spectrometer
   ////////////////////////////////////////////////////////////////////////////

   	int specIndex = 0;
   	if(seabreeze_open_spectrometer(specIndex, &error))
   	{
       	logger("no devices found.");
       	exit(1);
   	}

   ////////////////////////////////////////////////////////////////////////////
   // describe the unit we're testing
   ////////////////////////////////////////////////////////////////////////////

   	char type[MAX_LABEL_SIZE + 1];
   	seabreeze_get_model(specIndex, &error, type, sizeof(type));
   	if (check_error(specIndex, &error, "seabreeze_get_model"))
       	exit(1);

   	int pixels = seabreeze_get_formatted_spectrum_length(specIndex, &error);
   	if (check_error(specIndex, &error, "seabreeze_get_formatted_spectrum_length"))
       	exit(1);

   	logger("Testing index 0 (%s with %d pixels)", type, pixels);

   ////////////////////////////////////////////////////////////////////////////
   // Getting parameters for the run of the experiment			      //
   ////////////////////////////////////////////////////////////////////////////

int test = 0; unsigned scans_to_average = 0; unsigned integ_time_millis = 0; unsigned iterations = 0; unsigned size_time_step = 0; char answer; char fileName[100]; while(test < 100) { printf("\nEnter Your File name for csv(with .csv): "); scanf("%s", fileName);

printf("\nEnter integration time (millisec): "); scanf("%u", &integ_time_millis);

printf("Enter scans to average: "); scanf("%u", &scans_to_average); printf("\n");

printf("Enter number of iterations you wish: "); scanf("%u", &iterations); printf("\n");

printf("Enter the time between measures in seconds: "); scanf("%u", &size_time_step); printf("\n");

printf("This corresponds to a total time in minutes of:%u and in hours:%u \n", (iterations*size_time_step)/60, (iterations*size_time_step)/3600);

// this is just to check or restart entrance of parameters printf("Do you wish to proceed (y or n or q) ?: \n"); scanf(" %c", &answer); printf("\n"); if (answer == 'y') { test = 200; } else if (answer == 'q') { exit(0); } else { test++; }

}

   ////////////////////////////////////////////////////////////////////////////
   // configure all arrays 						     //
   ///////////////////////////////////////////////////////////////////////////

// the integration time is how much time a pixel is "open" it have to be low enough for the device not to saturate seabreeze_set_integration_time_microsec(specIndex, &error, integ_time_millis * 1000);

   	check_error(specIndex, &error, "seabreeze_set_integration_time_microsec");
   	double *spectrum    = (double*) malloc(pixels * sizeof(double));
   	double *average     = (double*) malloc(pixels * sizeof(double));
   	double *wavelengths = (double*) malloc(pixels * sizeof(double));

double *storage = (double*) malloc(iterations * sizeof(double));

seabreeze_get_wavelengths(specIndex, &error, wavelengths, pixels); check_error(specIndex, &error, "seabreeze_get_wavelengths");

/////////////////////////////////////////////////////////////////////////// // Running the loop for the length of the experiment /// /////////////////////////////////////////////////////////////////////////// for (unsigned u= 0; u < iterations; u++) { // memset sets all values of average to 0 memset(average, 0, pixels * sizeof(double)); // this wil run and output the average of multiple scans for (int i = 0; i < scans_to_average; i++) { memset(spectrum, 0, pixels * sizeof(double)); // gets the whole spectrum of the device seabreeze_get_formatted_spectrum(specIndex, &error, spectrum, pixels); for (unsigned j = 0; j < pixels; j++) { average[j] += spectrum[j]; } }

for (unsigned i = 0; i < pixels; i++) { average[i] /= scans_to_average; } double avrge = 0; double count = 0;

//////////////////////////////////////////////////////////////// // Initilisation of GNUPLOT session // ////////////////////////////////////////////////////////////////

//creating the Gnuplot objetcs gnuplot_ctrl * h1; gnuplot_ctrl * h2; // intilizing gnuplot sessions h1 = gnuplot_init(); h2 = gnuplot_init(); // setting x and y labels for the two sessions gnuplot_set_xlabel(h1,"t (in minutes)"); gnuplot_set_ylabel(h1, "OD600"); gnuplot_set_xlabel(h2,"t (in minutes)"); gnuplot_set_ylabel(h2, "OD600"); // setting gnuplot session to output gif at given size gnuplot_cmd(h2, "set terminal gif size 800,600 "); // setting gnuplot session to output using the x11 window manager

		gnuplot_cmd(h1,"set terminal x11");

// setting grid lines on the plots of both sessions gnuplot_cmd(h1,"set grid ytics lc rgb "#bbbbbb" lw 1 lt 0"); gnuplot_cmd(h1,"set grid xtics lc rgb "#bbbbbb" lw 1 lt 0"); gnuplot_cmd(h2,"set grid ytics lc rgb "#bbbbbb" lw 1 lt 0"); gnuplot_cmd(h2,"set grid xtics lc rgb "#bbbbbb" lw 1 lt 0"); // saving the output of one gnuplot session to a directory gnuplot_cmd(h2, "set output \'/home/pi/public_html/output.gif\'");

/* selects wavelenghts 595nm & 605nm contained between positions 542 & 601 of array average(this depends on the spectrometer)*/ for (unsigned i = 542; i < 601; i++) { avrge = avrge + average[i]; count = count + 1; } // this initializes the whole array that is being plotted to a blank at t = 0 if(u == 0) { storage = blank(storage, 10000/(avrge/count), iterations); } // this shifts the array to the left and inserts the latest value on the right else { storage = shiftarray(storage, 10000/(avrge/count), iterations); }

// plotting the arrays using the plot_x function of gnuplot_i library gnuplot_plot_x(h2, storage, iterations, "OD") ; gnuplot_plot_x(h1, storage, iterations, "OD") ;

fprintf(stderr, "OD 600 : %.6lf\n", avrge/count); // sleeps the amount of time between timesteps sleep(size_time_step); // creates a csv that can be read by gnuplot for future gnuplot gnuplot_write_x_csv(fileName,storage,iterations,"Overnight" ); // closing the gnuplot sessions (necessary to close the windows on the windows manager gnuplot_close(h1); gnuplot_close(h2);

}

   ////////////////////////////////////////////////////////////////////////////
   // cleanup
   ////////////////////////////////////////////////////////////////////////////

free(storage); free(average);

   	free(spectrum);
   	seabreeze_close_spectrometer(specIndex, &error);

}

double * shiftarray(double *old_array, double new_value, int size_array) { for(unsigned i = 1; i < size_array; i++) { old_array[i-1] = old_array[i];

} old_array[size_array-1] = new_value; return old_array; }

double * blank(double *stor_array, double value, int size_array) { for(unsigned i = 0; i < size_array ; i++) { stor_array[i] = value; } return stor_array; } </syntaxhighlight>