Sorbonne 2 firmware

Files at this revision

API Documentation at this revision

Comitter:
marcbax
Date:
Mon Jul 25 11:52:02 2011 +0000
Commit message:
V0.70 as delivered on July 25th

Changed in this revision

Servo.lib Show annotated file Show diff for this revision Revisions of this file
main.cpp Show annotated file Show diff for this revision Revisions of this file
main_070.cpp Show annotated file Show diff for this revision Revisions of this file
mbed.bld Show annotated file Show diff for this revision Revisions of this file
diff -r 000000000000 -r 0993f4cf5312 Servo.lib
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Servo.lib	Mon Jul 25 11:52:02 2011 +0000
@@ -0,0 +1,1 @@
+http://mbed.org/users/simon/code/Servo/#36b69a7ced07
diff -r 000000000000 -r 0993f4cf5312 main.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/main.cpp	Mon Jul 25 11:52:02 2011 +0000
@@ -0,0 +1,593 @@
+//Firmware to drive Sorbonne-2 bee training module
+char* fwversion = "0.70";                                          //For published versions use format "n.nn"
+                                                                   //For development versions add "D" to end of string
+//This version published on 25/07/2011
+
+#include "mbed.h"
+#include "Servo.h"
+
+DigitalOut led1(LED1), led2(LED2), led3(LED3), led4(LED4);
+DigitalOut lidclose(p5), lidlift(p6);
+DigitalOut clamp(p7), unclamp(p8);
+DigitalOut lockr(p12), unlockl(p13), lockl(p14), unlockr(p26);
+AnalogIn viclamp(p15);
+AnalogIn vswdetect(p16);
+AnalogIn adc4(p17);
+AnalogOut irLED(p18);
+AnalogIn vtemp(p19);
+AnalogIn ptor(p20);
+Servo arm(p21), elbow(p22);
+DigitalOut fan(p23);
+I2C beeholder(p9, p10);
+DigitalOut bhsel(p11);
+Serial acucomms(p28, p27);
+DigitalIn tmselect(p29);
+DigitalOut airswitcher(p25), spare1(p24);
+LocalFileSystem local("local");                                     //allow access to the mbed "thumbdrive" as a file system
+//FILE *calfile = fopen("/local/calfile.ini","w");                    //file used to store bee holder calibration values
+FILE *logfile = fopen("/local/sorb2log.csv","w");                   //creates new file sorb2log.csv and set for writing. Overwrites existing file!
+
+//Definition of global constants
+    //Training module PCB #2 robot arm positions
+    //Increase in arm position moves arm away from bee holder
+    //Increase in elbow position lowers tip
+    float armbasepos = 0.81;
+    float elbowbasepos = 0.6;
+    float armdippos = 0.81;
+    float elbowdippos = 0.84;
+    float armticklepos = 0.15;
+    float elbowticklepos = 0.63;
+    float armfeedpos = 0.08;
+    float elbowfeedpos = 0.77;
+    
+    //robot arm hold and move times                                 //all times are in seconds
+    float diptime = 1;                                              //time that brush stays down dipped in sugar water
+    float tickletimeout = 3;                                        //maximum time to tickle if no PER is detected
+    float feedtime = 3;                                             //feeding time
+    
+    //PER detection parameters
+    float calsetval = 1.4;                                          //voltage to which phototransistor output will be calibrated  
+    float PERsetval = 2.1;                                          //phototransistor output needs to be above this voltage for PER
+    float PERtime = 0.2;                                            //phototransistor output needs to stay high this long in seconds
+    
+    //Protocols
+    int addr = 0xA2;                                                //I2C address is actually 0x51, but mbed expects left-shifted address
+    int I2Cfreq = 10000;                                            //I2C bus frequency
+    int baudrate = 19200;                                           //baudrate of serial connection to ACU
+    
+//Definition of global variables
+
+struct holderrecord {                                               //used to hold data on beeholder
+    int serialno;                                                   //beeholder serial number 0-9999
+    float calvalue;                                                 //IR-LED calibration value
+    char cycleno;                                                   //number of cycles gone through in this session
+    char reslastcycle;                                              //result of last cycle, 1 for PER
+    char ticklenextcycle;                                           //whether tickling was done for last cycle
+    time_t tstamp;                                                  //timestamp when last cycle was run
+};
+
+holderrecord currentholder;                                         //struct record for the current beeholder
+holderrecord sessionrecord[101];                                    //sessionrecord contains holderrecords for up to 100 beeholders
+
+int numbeeholders;                                                  //number of beeholders used in current session
+int serialnum;
+char comchar;                                                       //serial command character for module control
+float fanspeed;
+bool lockstatus, clampstatus, lidstatus;                            //are true when locked, clamped or closed
+char swstatus;                                                      //4-bit number to indicate status of 4 detect switches
+float swvalue;                                                      //ADC value for detect switch voltage
+
+//Function declarations
+
+//Initialises sessionrecords
+void sessionrecordinit() {
+    for (int i=0; i<101; i++) {                                      //set base values for all possible beeholders
+        sessionrecord[i].serialno = 0;                              //set serialno to 0 so we can detect a unresponsive holder
+        sessionrecord[i].calvalue = 0;
+        sessionrecord[i].cycleno = 0;
+        sessionrecord[i].reslastcycle = 0;
+        sessionrecord[i].ticklenextcycle = 1;                       //default is to tickle on each cycle
+    }
+}
+
+//Reads serial numbers and calibration values from calfile.ini
+void getcaldata() {
+
+}
+
+//Initialise at power-up or reset
+void init_tm() {
+    led1=led2=led3=0;
+    led4=1;
+    lidclose=lidlift=0;
+    clamp=unclamp=0;
+    lockr=unlockr=lockl=unlockl=0;
+    irLED=0;
+    bhsel=0;
+    airswitcher=0;
+    spare1=0;
+    fan=0;
+    acucomms.baud(baudrate);
+    beeholder.frequency(I2Cfreq);
+    comchar=0;
+    lockstatus=0;
+    numbeeholders=0;
+    sessionrecordinit();
+    acucomms.printf("\n\r\rFirmware version: %s", fwversion);
+}
+
+//Converts the last 4 digits in the serial number string into a integer 0-9999
+int serialstring2int(char bser[8]) {
+    int tempserial = 0;    
+    tempserial = tempserial + (bser[4]-0x30)*1000;                  //5th digit is thousands
+    tempserial = tempserial + (bser[5]-0x30)*100;                   //6th digit is hundreds
+    tempserial = tempserial + (bser[6]-0x30)*10;                    //7th digit is tens
+    tempserial = tempserial + (bser[7]-0x30);                       //8th digit is units
+    return tempserial;
+}
+
+//beeholder resets on rising edge of select line
+void resetbeeholder() {                                             //need this as mounting beeholder causes undefined start of beeholder firmware
+    bhsel = 0;
+    wait(0.1);
+    bhsel = 1;
+    wait(0.3);
+}
+
+//gets holderrecord index for the holder with a certain serial number
+int getholderindex(int serialno) {
+    for (int i=1; i<=100; i++) {                                    //reverse lookup of index for a certain serial number
+        if (sessionrecord[i].serialno == serialno) return i;
+    }
+    return 0;                                                       //if the record is not found, returns i==0
+}
+
+//Reads beeholder serial number
+int getserialno() {
+    char bser[8];                                                   //define 8-byte serial number string to read
+    resetbeeholder();                                               //does not work without this!!
+    for (int i=0;i<8;i++) bser[i]=0x30;
+    bhsel = 0;                                                      //pull select line low
+    wait(0.2);
+    beeholder.stop();                                               //I2C stop condition
+    wait(0.2);                                                      //delay for beeholder to respond
+    beeholder.write(addr,0x0,1);                                    //initial write before read
+    beeholder.read(addr,bser,8);                                    //read 8 byte serial number
+    bhsel = 1;                                                      //pull select line high
+    int serialno = serialstring2int(bser);                          //translate serial number string to integer
+    return serialno;
+}
+
+//Returns 1 if a PER is detected within timeout seconds
+int detectPER(float timeout) {
+    Timer ttotal, tper;
+    ttotal.start();                                                 //start timers for time-out and PER-detect
+    ttotal.reset();
+    tper.start();
+    tper.reset();
+    while ((ttotal.read() < timeout) && (tper.read() < PERtime)) {  //loop until timeout or PER detected
+        wait_ms(10);
+        if (ptor * 3.3 < PERsetval) tper.reset();                   //if phototransistor voltage below treshold keep PER timer in reset
+                                                                    //if above treshold let timer run until it reaches PERtime
+    }
+    ttotal.stop();
+    tper.stop();
+    return (tper.read() >= PERtime);                                //if the loop exit condition was a PER, return a TRUE value
+}
+
+//Function performs beeholder/IR-led calibration
+float calibrate(int runs) {
+    float tempcal, ptorhold;
+    tempcal=0.5;                                                    //start calibration at 50% voltage
+    irLED=tempcal;
+    float calstep;                                                  //start calstep at 25% voltage
+    calstep = tempcal/2;
+    //acucomms.printf("\n\rInitial calibration:");
+    for (int i=0; i<10; i++) {                                      //does a "10-bit binary search" for the correct voltage to get a good response
+        irLED = tempcal;
+        wait(0.1);                                                 //important to allow AD converter to settle
+        ptorhold=ptor;
+        //acucomms.printf("\n\r%5.3f - %5.3f", tempcal, ptorhold);
+        if (ptorhold < calsetval/3.3) {                                //check phototransistor voltage against desired value
+            tempcal = tempcal - calstep;                            //if phototransistor voltage is too low then reduce brightness
+        }
+        else {
+            tempcal = tempcal + calstep;                            //if phototransistor voltage is too high then increase brightness
+        }
+        calstep = calstep/2;                                        //on each loop of the for-cycle make smaller changes to IR LED voltage
+    }
+    float calib;
+    calib = tempcal;                                                //set preliminary calibration to the value just measured
+    for (int j=1; j<runs; j++) {                                    //run another j-1 runs, this corrects for antennae-movement as
+        tempcal=0.5;                                                //we use the lowest calibration value from j runs
+        irLED=tempcal;                                              //this is similar to what we do in the cassettes
+        calstep = tempcal/2;
+        for (int i=0;i<10;i++) {
+            irLED = tempcal;
+            wait(0.1);
+            ptorhold=ptor;
+            if (ptorhold < calsetval/3.3) {
+                tempcal = tempcal - calstep;
+            }
+            else {
+                tempcal = tempcal + calstep;
+            }
+            calstep = calstep/2;
+        }
+        if (tempcal < calib) calib = tempcal;                       //use the lowest of j calibration values
+    }
+    irLED = 0;
+    return calib;
+}
+
+//switches the IR LED on at the right brightness level for the beeholder
+void IRledON(int i) {
+    irLED = sessionrecord[i].calvalue;
+}
+ 
+//moves arm to a position in a specified time, allowing speed control
+void armmove (float endpos, float movetime) {
+    float startpos = arm.read();
+    int numsteps = (movetime * 50);                                 //50 pulses/second, so each step is 1 servo pulse
+    for (int i=0; i<numsteps; i++) {
+        arm = startpos + i * (endpos - startpos)/numsteps;
+        wait(movetime/numsteps);
+    }
+    arm = endpos;
+}
+
+//moves elbow to a position in a specified time, allowing speed control
+void elbowmove (float endpos, float movetime) {
+    float startpos = elbow.read();
+    int numsteps = (movetime * 50);                                 //50 pulses/second, so each step is 1 servo pulse
+    for (int i=0; i<numsteps; i++) {
+        elbow = startpos + i * (endpos - startpos)/numsteps;
+        wait(movetime/numsteps);
+    }
+    elbow = endpos;
+}
+
+//Performs a conditioning cycle. if tickle==0, no tickling takes place. Return==1 if a PER has been detected
+int condcycle(int tickle) {
+    int perseen;
+    perseen = 0;
+    //dip brush
+    armmove(armdippos, 0.5);
+    elbowmove(elbowdippos, 0.3);
+    wait(diptime);
+    elbowmove(elbowbasepos, 0.3);
+    armmove(armbasepos, 0.5);
+    airswitcher=1;                                              //switch air to target odour
+    //tickle
+    if (tickle) {                                               //if tickling, first tickle then wait for PER or timeout
+        elbowmove(elbowticklepos, 0.2);
+        armmove(armticklepos, 1.5);                             //slower move of arm towards bee
+        perseen = detectPER(tickletimeout);                     //tickle until timeout or PER detected
+    }
+    //or not tickle
+    else {
+        perseen = detectPER(tickletimeout);                     //if not tickling, wait for PER or timeout then move to pre-feeding position
+        armmove(armticklepos-0.05, 1);                          //move to position between LED and holder
+        elbowmove(elbowticklepos, 0.3);
+    }
+    //feeding only if you have tickled or a PER has been detected
+    if (tickle || perseen) {                                    //only feed if a PER has been detector, or "tickle" is true
+        elbowmove(elbowfeedpos, 0.3);
+        armmove(armfeedpos, 0.3);
+        wait(feedtime);
+        armmove(armticklepos -0.05, 0.3);
+        elbowmove(elbowticklepos, 0.3);
+    }
+    //move back to base position
+    airswitcher=0;                                              //switch back to clean air
+    armmove(armbasepos, 0.5);                                   //back to basepos
+    elbowmove(elbowbasepos, 0.3);                               //
+    return perseen;
+}
+
+
+char switchstatus(float vswdetect) {
+    //outputs char (4-bit flag) to reflect positions of 4 detect switches
+    if (vswdetect>0.38 && vswdetect<0.4) return 11;
+    if (vswdetect>0.4 && vswdetect<0.45) return 9;
+    if (vswdetect>0.45 && vswdetect<0.49) return 10;
+    if (vswdetect>0.49 && vswdetect<0.54) return 8;
+    if (vswdetect>0.54 && vswdetect<0.58) return 7;
+    if (vswdetect>0.58 && vswdetect<0.62) return 5;
+    if (vswdetect>0.62 && vswdetect<0.66) return 3;
+    if (vswdetect>0.66 && vswdetect<0.74) return 1;
+    if (vswdetect>0.74 && vswdetect<0.8) return 6;
+    if (vswdetect>0.8 && vswdetect<0.85) return 4;
+    if (vswdetect>0.85 && vswdetect<0.95) return 2;
+    if (vswdetect>0.95 && vswdetect<1.01) return 0;
+    return 16;
+}
+
+//Clamp bee holder
+void clampholder() {
+    unclamp=1;
+    wait(4);
+    unclamp=0;
+}
+
+//Unclamp bee holder
+void unclampholder() {
+    clamp=1;
+    wait(1);
+    clamp=0;
+}
+
+//Lift lid
+void liftlid() {
+    bool notup;
+    notup=1;
+    lidclose=1;
+    while (notup) {
+        wait(0.01);
+        notup = (switchstatus(vswdetect.read()) != 7);
+    }
+    lidclose=0;
+    lidstatus=0;
+}
+
+//Close lid
+void closelid() {
+    bool notdown;
+    notdown=1;
+    lidlift=1;
+    while (notdown) {
+        wait(0.01);
+        notdown = (switchstatus(vswdetect.read()) != 11);
+    }
+    lidlift=0;
+    lidstatus=1;
+}
+
+//Lock lid
+void locklid() {
+    wait(0.1);
+}
+
+//Unlock lid
+void unlocklid() {
+    wait(0.1);
+}
+
+//Set date and time
+void setdatetime() {
+    
+
+}
+
+
+void registerbeeholder() {
+    //registers and calibrates the bee holder currently clamped
+    int serialno, i;
+    float calvalue;
+    serialno = getserialno();
+    i = getholderindex(serialno);
+    if (i == 0) {
+        numbeeholders++;
+        if (numbeeholders == 101) {
+            acucomms.printf("Number of holders exceeds 100");
+        }
+        else {
+            sessionrecord[numbeeholders].serialno = serialno;
+            calvalue = calibrate(5);
+            if (calvalue < 0.98 && calvalue > 0.25) {
+                sessionrecord[numbeeholders].calvalue = calvalue;
+                acucomms.printf("\n\rCal %4u - %4.2fV", serialno, calvalue*3.3);
+            }
+            else {
+                acucomms.printf("\n\rCal %4u - invalid", serialno);
+            }
+        }
+    }
+}
+
+/*
+//Registers and calibrates all beeholders used in this session
+int registerbeeholders() {
+    int i;
+    bool done;
+    char buffert[30];
+    i = done = 0;
+    //cleardisplay();                                                 //clear screen and home cursor
+    fprintf(logfile, "calibration record:\r");
+    fprintf(logfile, "i, serialno, LED V, time\r");
+    while (i<30 && !done) {                                         //register and calibrate a maximum of 30 beeholders
+        //display.printf("calibrating %u\r",i+1);
+        sessionrecord[i].serialno = getserialno();           //read serial number
+        if (sessionrecord[i].serialno != 0) {                       //check if serial number correctly read - if not it will be 0000
+            sessionrecord[i].calvalue = calibrate(station, 5);      //5 calibration cycles
+            if ((sessionrecord[i].calvalue > 0.25) && (sessionrecord[i].calvalue < 0.97)) {     //check that calvalue is in expected range
+                sessionrecord[i].tstamp = time(NULL);                   //create timestamp NOW
+                strftime(buffert, 20, "%X", localtime(&sessionrecord[i].tstamp));               //formats time part of timestamp
+                cleardisplay();
+                display.printf("SN %4u - cal %4.2fV\r", sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3);
+                display.printf("OK for next\r");
+                display.printf("DOWN for training");
+                fprintf(logfile, "%4u,%6u,%6.2f,  %s,  calibrated\r", i, sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3, buffert);
+                i++;
+            }
+            else {
+                cleardisplay();
+                display.printf("SN %4u - cal %4.2fV\r", sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3);
+                display.printf("Cal out of range!\r");
+                multibeeps(2,0.5);
+                display.printf("OK to recalibrate\r");
+                fprintf(logfile, "%4u,%6u,%6.2f,  %s,  out of range\r", i, sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3, buffert);
+            }
+            while (!done && oksw) {                                 //loop until OK or DOWN are pressed
+                wait(0.02);
+                done = !dnsw;                                       //DOWN exits registration cycle and moves to training
+            }
+        }
+        else {                                                      //retry when serialno can't be read (is 0000)
+            cleardisplay();
+            multibeeps(3,0.3);                                      //beep-beep-beep when beeholder not correctly read
+            display.printf("invalid serial no\r");
+            display.printf("reseat beeholder\r");
+            display.printf("press OK");
+            while (oksw) wait(0.02);                                //loop until OK is pressed to start calibration loop again
+        }
+        cleardisplay();
+    }
+    return i;                                                       //upon done condition, i== number of beeholders calibrated
+}
+
+*/
+
+float calcairtemp(float vntc) {
+    return 0.1;
+}
+
+//all the elements making up a single training cycle with one beeholder
+void trainingcycle() {
+    wait(0.2);
+    time_t tstamp = time(NULL);                                     //create timestamp NOW
+    char buffert[30];
+    strftime(buffert, 20, "%X", localtime(&tstamp));                //format timestamp to time string
+    int serialno;
+    serialno = getserialno();
+    int i = getholderindex(serialno);                               //get index i for serial number
+    if (i != 0) {
+        IRledON(i);                                                     //switch IR LED on at correct brightness
+        sessionrecord[i].cycleno++;                                     //increment cycle number for this beeholder
+        acucomms.printf("\n\rSN: %4u, cycle %u - ", serialno, sessionrecord[i].cycleno);
+        sessionrecord[i].reslastcycle = condcycle(sessionrecord[i].ticklenextcycle);       //do a conditioning cycle
+        fprintf(logfile, "%s,",buffert);
+        fprintf(logfile, "  %4u,",serialno);
+        fprintf(logfile, "  %2u,", sessionrecord[i].cycleno);
+        if (sessionrecord[i].reslastcycle) {                            //log PER or TimeOut
+            fprintf(logfile, "  PER,");
+        }
+        else {
+            fprintf(logfile, "   TO,");
+        }
+        fprintf(logfile, " training\r");
+        if (sessionrecord[i].reslastcycle) {
+            acucomms.printf("PER detected");
+        }
+        else {
+            acucomms.printf("PER time-out");
+        }
+    }
+    else {
+        acucomms.printf("\n\rBee holder %4u not registered", serialno);
+    }
+}
+
+
+
+int main() {
+    init_tm();
+    while (comchar != 88) {
+        comchar = acucomms.getc();
+        switch (comchar) {
+        case 65: //"A"
+            //Continue after pause
+            break;
+        case 66: //"B"
+            //Register bee holder
+            registerbeeholder();
+            break;
+        case 67: //"C"
+            //Calibrate bee holder
+            acucomms.printf("\r\nCalibration: %5.3f", calibrate(5));
+            break;
+        case 68: //"D"
+            //Clamp bee holder
+            clampholder();
+            break;
+        case 69: //"E"
+            //Unclamp bee holder
+            unclampholder();
+            break;
+        case 70: //"F"
+            //Open lid
+            liftlid();
+            break;
+        case 71: //"G"
+            //Close lid
+            closelid();
+            break;
+        case 72: //"H"
+            //Lock lid
+            locklid();
+            break;
+        case 73: //"I"
+            //Unlock lid
+            unlocklid();
+            break;
+        case 74: //"J"
+            //Conduct training cycle
+            trainingcycle();
+            break;
+        case 75: //"K"
+            //Read air temperature
+            break;
+        case 76: //"L"
+            //Toggle fan on/off
+            fan=!fan;
+            break;
+        case 77: //"M"
+            //Move arm/elbow to basepos
+            armmove(armbasepos, 1);
+            elbowmove(elbowbasepos, 1);
+            break;
+        case 78: //"N"
+            //Move arm/elbow to dippos
+            armmove(armdippos, 1);
+            elbowmove(elbowdippos, 1);
+            break;
+        case 79: //"O"
+            //Move arm/elbow to ticklepos
+            armmove(armticklepos, 1);
+            elbowmove(elbowticklepos, 1);
+            break;
+        case 80: //"P"
+            //Move arm/elbow to feedpos
+            armmove(armfeedpos, 1);
+            elbowmove(elbowfeedpos, 1);
+            break;
+        case 81: //"Q"
+            //Print SWdetect value
+            wait(0.1);
+            swvalue = vswdetect.read();
+            acucomms.printf("\rVSWDETECT: %5.3f", swvalue);
+            break;
+        case 82: //"R"
+            //multiple calibrations to see variation
+            acucomms.printf("\r\nBee holder: %4u", getserialno());
+            for (int i=0; i<40; i++) {
+                acucomms.printf("\r\nN%3u C=%5.3f", i+1, calibrate(5));
+                wait(15);
+            }
+            acucomms.printf("\r\nDone");
+            break;
+        case 83: //"S"
+            //Toggle air switcher
+            airswitcher = !airswitcher;
+            if (airswitcher) {
+                acucomms.printf("\n\rAirswitcher on");
+            }
+            else {
+                acucomms.printf("\n\rAirswitcher off");
+            }
+            break;
+        case 84: //"T"
+            //set date and time on RTC
+            setdatetime();
+            break;
+        default: //All other characters
+            //Do nothing
+            break;
+        }
+        if (comchar != 88) comchar=0;
+    }
+    acucomms.printf("\n\rSession closed");
+    //Close logfile
+    fprintf(logfile, "session closed");
+    fclose(logfile);                                                //close logfile for reading    
+}
diff -r 000000000000 -r 0993f4cf5312 main_070.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/main_070.cpp	Mon Jul 25 11:52:02 2011 +0000
@@ -0,0 +1,593 @@
+//Firmware to drive Sorbonne-2 bee training module
+char* fwversion = "0.70";                                          //For published versions use format "n.nn"
+                                                                   //For development versions add "D" to end of string
+//This version published on 25/07/2011
+
+#include "mbed.h"
+#include "Servo.h"
+
+DigitalOut led1(LED1), led2(LED2), led3(LED3), led4(LED4);
+DigitalOut lidclose(p5), lidlift(p6);
+DigitalOut clamp(p7), unclamp(p8);
+DigitalOut lockr(p12), unlockl(p13), lockl(p14), unlockr(p26);
+AnalogIn viclamp(p15);
+AnalogIn vswdetect(p16);
+AnalogIn adc4(p17);
+AnalogOut irLED(p18);
+AnalogIn vtemp(p19);
+AnalogIn ptor(p20);
+Servo arm(p21), elbow(p22);
+DigitalOut fan(p23);
+I2C beeholder(p9, p10);
+DigitalOut bhsel(p11);
+Serial acucomms(p28, p27);
+DigitalIn tmselect(p29);
+DigitalOut airswitcher(p25), spare1(p24);
+LocalFileSystem local("local");                                     //allow access to the mbed "thumbdrive" as a file system
+//FILE *calfile = fopen("/local/calfile.ini","w");                    //file used to store bee holder calibration values
+FILE *logfile = fopen("/local/sorb2log.csv","w");                   //creates new file sorb2log.csv and set for writing. Overwrites existing file!
+
+//Definition of global constants
+    //Training module PCB #2 robot arm positions
+    //Increase in arm position moves arm away from bee holder
+    //Increase in elbow position lowers tip
+    float armbasepos = 0.81;
+    float elbowbasepos = 0.6;
+    float armdippos = 0.81;
+    float elbowdippos = 0.84;
+    float armticklepos = 0.15;
+    float elbowticklepos = 0.63;
+    float armfeedpos = 0.08;
+    float elbowfeedpos = 0.77;
+    
+    //robot arm hold and move times                                 //all times are in seconds
+    float diptime = 1;                                              //time that brush stays down dipped in sugar water
+    float tickletimeout = 3;                                        //maximum time to tickle if no PER is detected
+    float feedtime = 3;                                             //feeding time
+    
+    //PER detection parameters
+    float calsetval = 1.4;                                          //voltage to which phototransistor output will be calibrated  
+    float PERsetval = 2.1;                                          //phototransistor output needs to be above this voltage for PER
+    float PERtime = 0.2;                                            //phototransistor output needs to stay high this long in seconds
+    
+    //Protocols
+    int addr = 0xA2;                                                //I2C address is actually 0x51, but mbed expects left-shifted address
+    int I2Cfreq = 10000;                                            //I2C bus frequency
+    int baudrate = 19200;                                           //baudrate of serial connection to ACU
+    
+//Definition of global variables
+
+struct holderrecord {                                               //used to hold data on beeholder
+    int serialno;                                                   //beeholder serial number 0-9999
+    float calvalue;                                                 //IR-LED calibration value
+    char cycleno;                                                   //number of cycles gone through in this session
+    char reslastcycle;                                              //result of last cycle, 1 for PER
+    char ticklenextcycle;                                           //whether tickling was done for last cycle
+    time_t tstamp;                                                  //timestamp when last cycle was run
+};
+
+holderrecord currentholder;                                         //struct record for the current beeholder
+holderrecord sessionrecord[101];                                    //sessionrecord contains holderrecords for up to 100 beeholders
+
+int numbeeholders;                                                  //number of beeholders used in current session
+int serialnum;
+char comchar;                                                       //serial command character for module control
+float fanspeed;
+bool lockstatus, clampstatus, lidstatus;                            //are true when locked, clamped or closed
+char swstatus;                                                      //4-bit number to indicate status of 4 detect switches
+float swvalue;                                                      //ADC value for detect switch voltage
+
+//Function declarations
+
+//Initialises sessionrecords
+void sessionrecordinit() {
+    for (int i=0; i<101; i++) {                                      //set base values for all possible beeholders
+        sessionrecord[i].serialno = 0;                              //set serialno to 0 so we can detect a unresponsive holder
+        sessionrecord[i].calvalue = 0;
+        sessionrecord[i].cycleno = 0;
+        sessionrecord[i].reslastcycle = 0;
+        sessionrecord[i].ticklenextcycle = 1;                       //default is to tickle on each cycle
+    }
+}
+
+//Reads serial numbers and calibration values from calfile.ini
+void getcaldata() {
+
+}
+
+//Initialise at power-up or reset
+void init_tm() {
+    led1=led2=led3=0;
+    led4=1;
+    lidclose=lidlift=0;
+    clamp=unclamp=0;
+    lockr=unlockr=lockl=unlockl=0;
+    irLED=0;
+    bhsel=0;
+    airswitcher=0;
+    spare1=0;
+    fan=0;
+    acucomms.baud(baudrate);
+    beeholder.frequency(I2Cfreq);
+    comchar=0;
+    lockstatus=0;
+    numbeeholders=0;
+    sessionrecordinit();
+    acucomms.printf("\n\r\rFirmware version: %s", fwversion);
+}
+
+//Converts the last 4 digits in the serial number string into a integer 0-9999
+int serialstring2int(char bser[8]) {
+    int tempserial = 0;    
+    tempserial = tempserial + (bser[4]-0x30)*1000;                  //5th digit is thousands
+    tempserial = tempserial + (bser[5]-0x30)*100;                   //6th digit is hundreds
+    tempserial = tempserial + (bser[6]-0x30)*10;                    //7th digit is tens
+    tempserial = tempserial + (bser[7]-0x30);                       //8th digit is units
+    return tempserial;
+}
+
+//beeholder resets on rising edge of select line
+void resetbeeholder() {                                             //need this as mounting beeholder causes undefined start of beeholder firmware
+    bhsel = 0;
+    wait(0.1);
+    bhsel = 1;
+    wait(0.3);
+}
+
+//gets holderrecord index for the holder with a certain serial number
+int getholderindex(int serialno) {
+    for (int i=1; i<=100; i++) {                                    //reverse lookup of index for a certain serial number
+        if (sessionrecord[i].serialno == serialno) return i;
+    }
+    return 0;                                                       //if the record is not found, returns i==0
+}
+
+//Reads beeholder serial number
+int getserialno() {
+    char bser[8];                                                   //define 8-byte serial number string to read
+    resetbeeholder();                                               //does not work without this!!
+    for (int i=0;i<8;i++) bser[i]=0x30;
+    bhsel = 0;                                                      //pull select line low
+    wait(0.2);
+    beeholder.stop();                                               //I2C stop condition
+    wait(0.2);                                                      //delay for beeholder to respond
+    beeholder.write(addr,0x0,1);                                    //initial write before read
+    beeholder.read(addr,bser,8);                                    //read 8 byte serial number
+    bhsel = 1;                                                      //pull select line high
+    int serialno = serialstring2int(bser);                          //translate serial number string to integer
+    return serialno;
+}
+
+//Returns 1 if a PER is detected within timeout seconds
+int detectPER(float timeout) {
+    Timer ttotal, tper;
+    ttotal.start();                                                 //start timers for time-out and PER-detect
+    ttotal.reset();
+    tper.start();
+    tper.reset();
+    while ((ttotal.read() < timeout) && (tper.read() < PERtime)) {  //loop until timeout or PER detected
+        wait_ms(10);
+        if (ptor * 3.3 < PERsetval) tper.reset();                   //if phototransistor voltage below treshold keep PER timer in reset
+                                                                    //if above treshold let timer run until it reaches PERtime
+    }
+    ttotal.stop();
+    tper.stop();
+    return (tper.read() >= PERtime);                                //if the loop exit condition was a PER, return a TRUE value
+}
+
+//Function performs beeholder/IR-led calibration
+float calibrate(int runs) {
+    float tempcal, ptorhold;
+    tempcal=0.5;                                                    //start calibration at 50% voltage
+    irLED=tempcal;
+    float calstep;                                                  //start calstep at 25% voltage
+    calstep = tempcal/2;
+    //acucomms.printf("\n\rInitial calibration:");
+    for (int i=0; i<10; i++) {                                      //does a "10-bit binary search" for the correct voltage to get a good response
+        irLED = tempcal;
+        wait(0.1);                                                 //important to allow AD converter to settle
+        ptorhold=ptor;
+        //acucomms.printf("\n\r%5.3f - %5.3f", tempcal, ptorhold);
+        if (ptorhold < calsetval/3.3) {                                //check phototransistor voltage against desired value
+            tempcal = tempcal - calstep;                            //if phototransistor voltage is too low then reduce brightness
+        }
+        else {
+            tempcal = tempcal + calstep;                            //if phototransistor voltage is too high then increase brightness
+        }
+        calstep = calstep/2;                                        //on each loop of the for-cycle make smaller changes to IR LED voltage
+    }
+    float calib;
+    calib = tempcal;                                                //set preliminary calibration to the value just measured
+    for (int j=1; j<runs; j++) {                                    //run another j-1 runs, this corrects for antennae-movement as
+        tempcal=0.5;                                                //we use the lowest calibration value from j runs
+        irLED=tempcal;                                              //this is similar to what we do in the cassettes
+        calstep = tempcal/2;
+        for (int i=0;i<10;i++) {
+            irLED = tempcal;
+            wait(0.1);
+            ptorhold=ptor;
+            if (ptorhold < calsetval/3.3) {
+                tempcal = tempcal - calstep;
+            }
+            else {
+                tempcal = tempcal + calstep;
+            }
+            calstep = calstep/2;
+        }
+        if (tempcal < calib) calib = tempcal;                       //use the lowest of j calibration values
+    }
+    irLED = 0;
+    return calib;
+}
+
+//switches the IR LED on at the right brightness level for the beeholder
+void IRledON(int i) {
+    irLED = sessionrecord[i].calvalue;
+}
+ 
+//moves arm to a position in a specified time, allowing speed control
+void armmove (float endpos, float movetime) {
+    float startpos = arm.read();
+    int numsteps = (movetime * 50);                                 //50 pulses/second, so each step is 1 servo pulse
+    for (int i=0; i<numsteps; i++) {
+        arm = startpos + i * (endpos - startpos)/numsteps;
+        wait(movetime/numsteps);
+    }
+    arm = endpos;
+}
+
+//moves elbow to a position in a specified time, allowing speed control
+void elbowmove (float endpos, float movetime) {
+    float startpos = elbow.read();
+    int numsteps = (movetime * 50);                                 //50 pulses/second, so each step is 1 servo pulse
+    for (int i=0; i<numsteps; i++) {
+        elbow = startpos + i * (endpos - startpos)/numsteps;
+        wait(movetime/numsteps);
+    }
+    elbow = endpos;
+}
+
+//Performs a conditioning cycle. if tickle==0, no tickling takes place. Return==1 if a PER has been detected
+int condcycle(int tickle) {
+    int perseen;
+    perseen = 0;
+    //dip brush
+    armmove(armdippos, 0.5);
+    elbowmove(elbowdippos, 0.3);
+    wait(diptime);
+    elbowmove(elbowbasepos, 0.3);
+    armmove(armbasepos, 0.5);
+    airswitcher=1;                                              //switch air to target odour
+    //tickle
+    if (tickle) {                                               //if tickling, first tickle then wait for PER or timeout
+        elbowmove(elbowticklepos, 0.2);
+        armmove(armticklepos, 1.5);                             //slower move of arm towards bee
+        perseen = detectPER(tickletimeout);                     //tickle until timeout or PER detected
+    }
+    //or not tickle
+    else {
+        perseen = detectPER(tickletimeout);                     //if not tickling, wait for PER or timeout then move to pre-feeding position
+        armmove(armticklepos-0.05, 1);                          //move to position between LED and holder
+        elbowmove(elbowticklepos, 0.3);
+    }
+    //feeding only if you have tickled or a PER has been detected
+    if (tickle || perseen) {                                    //only feed if a PER has been detector, or "tickle" is true
+        elbowmove(elbowfeedpos, 0.3);
+        armmove(armfeedpos, 0.3);
+        wait(feedtime);
+        armmove(armticklepos -0.05, 0.3);
+        elbowmove(elbowticklepos, 0.3);
+    }
+    //move back to base position
+    airswitcher=0;                                              //switch back to clean air
+    armmove(armbasepos, 0.5);                                   //back to basepos
+    elbowmove(elbowbasepos, 0.3);                               //
+    return perseen;
+}
+
+
+char switchstatus(float vswdetect) {
+    //outputs char (4-bit flag) to reflect positions of 4 detect switches
+    if (vswdetect>0.38 && vswdetect<0.4) return 11;
+    if (vswdetect>0.4 && vswdetect<0.45) return 9;
+    if (vswdetect>0.45 && vswdetect<0.49) return 10;
+    if (vswdetect>0.49 && vswdetect<0.54) return 8;
+    if (vswdetect>0.54 && vswdetect<0.58) return 7;
+    if (vswdetect>0.58 && vswdetect<0.62) return 5;
+    if (vswdetect>0.62 && vswdetect<0.66) return 3;
+    if (vswdetect>0.66 && vswdetect<0.74) return 1;
+    if (vswdetect>0.74 && vswdetect<0.8) return 6;
+    if (vswdetect>0.8 && vswdetect<0.85) return 4;
+    if (vswdetect>0.85 && vswdetect<0.95) return 2;
+    if (vswdetect>0.95 && vswdetect<1.01) return 0;
+    return 16;
+}
+
+//Clamp bee holder
+void clampholder() {
+    unclamp=1;
+    wait(4);
+    unclamp=0;
+}
+
+//Unclamp bee holder
+void unclampholder() {
+    clamp=1;
+    wait(1);
+    clamp=0;
+}
+
+//Lift lid
+void liftlid() {
+    bool notup;
+    notup=1;
+    lidclose=1;
+    while (notup) {
+        wait(0.01);
+        notup = (switchstatus(vswdetect.read()) != 7);
+    }
+    lidclose=0;
+    lidstatus=0;
+}
+
+//Close lid
+void closelid() {
+    bool notdown;
+    notdown=1;
+    lidlift=1;
+    while (notdown) {
+        wait(0.01);
+        notdown = (switchstatus(vswdetect.read()) != 11);
+    }
+    lidlift=0;
+    lidstatus=1;
+}
+
+//Lock lid
+void locklid() {
+    wait(0.1);
+}
+
+//Unlock lid
+void unlocklid() {
+    wait(0.1);
+}
+
+//Set date and time
+void setdatetime() {
+    
+
+}
+
+
+void registerbeeholder() {
+    //registers and calibrates the bee holder currently clamped
+    int serialno, i;
+    float calvalue;
+    serialno = getserialno();
+    i = getholderindex(serialno);
+    if (i == 0) {
+        numbeeholders++;
+        if (numbeeholders == 101) {
+            acucomms.printf("Number of holders exceeds 100");
+        }
+        else {
+            sessionrecord[numbeeholders].serialno = serialno;
+            calvalue = calibrate(5);
+            if (calvalue < 0.98 && calvalue > 0.25) {
+                sessionrecord[numbeeholders].calvalue = calvalue;
+                acucomms.printf("\n\rCal %4u - %4.2fV", serialno, calvalue*3.3);
+            }
+            else {
+                acucomms.printf("\n\rCal %4u - invalid", serialno);
+            }
+        }
+    }
+}
+
+/*
+//Registers and calibrates all beeholders used in this session
+int registerbeeholders() {
+    int i;
+    bool done;
+    char buffert[30];
+    i = done = 0;
+    //cleardisplay();                                                 //clear screen and home cursor
+    fprintf(logfile, "calibration record:\r");
+    fprintf(logfile, "i, serialno, LED V, time\r");
+    while (i<30 && !done) {                                         //register and calibrate a maximum of 30 beeholders
+        //display.printf("calibrating %u\r",i+1);
+        sessionrecord[i].serialno = getserialno();           //read serial number
+        if (sessionrecord[i].serialno != 0) {                       //check if serial number correctly read - if not it will be 0000
+            sessionrecord[i].calvalue = calibrate(station, 5);      //5 calibration cycles
+            if ((sessionrecord[i].calvalue > 0.25) && (sessionrecord[i].calvalue < 0.97)) {     //check that calvalue is in expected range
+                sessionrecord[i].tstamp = time(NULL);                   //create timestamp NOW
+                strftime(buffert, 20, "%X", localtime(&sessionrecord[i].tstamp));               //formats time part of timestamp
+                cleardisplay();
+                display.printf("SN %4u - cal %4.2fV\r", sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3);
+                display.printf("OK for next\r");
+                display.printf("DOWN for training");
+                fprintf(logfile, "%4u,%6u,%6.2f,  %s,  calibrated\r", i, sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3, buffert);
+                i++;
+            }
+            else {
+                cleardisplay();
+                display.printf("SN %4u - cal %4.2fV\r", sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3);
+                display.printf("Cal out of range!\r");
+                multibeeps(2,0.5);
+                display.printf("OK to recalibrate\r");
+                fprintf(logfile, "%4u,%6u,%6.2f,  %s,  out of range\r", i, sessionrecord[i].serialno, sessionrecord[i].calvalue*3.3, buffert);
+            }
+            while (!done && oksw) {                                 //loop until OK or DOWN are pressed
+                wait(0.02);
+                done = !dnsw;                                       //DOWN exits registration cycle and moves to training
+            }
+        }
+        else {                                                      //retry when serialno can't be read (is 0000)
+            cleardisplay();
+            multibeeps(3,0.3);                                      //beep-beep-beep when beeholder not correctly read
+            display.printf("invalid serial no\r");
+            display.printf("reseat beeholder\r");
+            display.printf("press OK");
+            while (oksw) wait(0.02);                                //loop until OK is pressed to start calibration loop again
+        }
+        cleardisplay();
+    }
+    return i;                                                       //upon done condition, i== number of beeholders calibrated
+}
+
+*/
+
+float calcairtemp(float vntc) {
+    return 0.1;
+}
+
+//all the elements making up a single training cycle with one beeholder
+void trainingcycle() {
+    wait(0.2);
+    time_t tstamp = time(NULL);                                     //create timestamp NOW
+    char buffert[30];
+    strftime(buffert, 20, "%X", localtime(&tstamp));                //format timestamp to time string
+    int serialno;
+    serialno = getserialno();
+    int i = getholderindex(serialno);                               //get index i for serial number
+    if (i != 0) {
+        IRledON(i);                                                     //switch IR LED on at correct brightness
+        sessionrecord[i].cycleno++;                                     //increment cycle number for this beeholder
+        acucomms.printf("\n\rSN: %4u, cycle %u - ", serialno, sessionrecord[i].cycleno);
+        sessionrecord[i].reslastcycle = condcycle(sessionrecord[i].ticklenextcycle);       //do a conditioning cycle
+        fprintf(logfile, "%s,",buffert);
+        fprintf(logfile, "  %4u,",serialno);
+        fprintf(logfile, "  %2u,", sessionrecord[i].cycleno);
+        if (sessionrecord[i].reslastcycle) {                            //log PER or TimeOut
+            fprintf(logfile, "  PER,");
+        }
+        else {
+            fprintf(logfile, "   TO,");
+        }
+        fprintf(logfile, " training\r");
+        if (sessionrecord[i].reslastcycle) {
+            acucomms.printf("PER detected");
+        }
+        else {
+            acucomms.printf("PER time-out");
+        }
+    }
+    else {
+        acucomms.printf("\n\rBee holder %4u not registered", serialno);
+    }
+}
+
+
+
+int main() {
+    init_tm();
+    while (comchar != 88) {
+        comchar = acucomms.getc();
+        switch (comchar) {
+        case 65: //"A"
+            //Continue after pause
+            break;
+        case 66: //"B"
+            //Register bee holder
+            registerbeeholder();
+            break;
+        case 67: //"C"
+            //Calibrate bee holder
+            acucomms.printf("\r\nCalibration: %5.3f", calibrate(5));
+            break;
+        case 68: //"D"
+            //Clamp bee holder
+            clampholder();
+            break;
+        case 69: //"E"
+            //Unclamp bee holder
+            unclampholder();
+            break;
+        case 70: //"F"
+            //Open lid
+            liftlid();
+            break;
+        case 71: //"G"
+            //Close lid
+            closelid();
+            break;
+        case 72: //"H"
+            //Lock lid
+            locklid();
+            break;
+        case 73: //"I"
+            //Unlock lid
+            unlocklid();
+            break;
+        case 74: //"J"
+            //Conduct training cycle
+            trainingcycle();
+            break;
+        case 75: //"K"
+            //Read air temperature
+            break;
+        case 76: //"L"
+            //Toggle fan on/off
+            fan=!fan;
+            break;
+        case 77: //"M"
+            //Move arm/elbow to basepos
+            armmove(armbasepos, 1);
+            elbowmove(elbowbasepos, 1);
+            break;
+        case 78: //"N"
+            //Move arm/elbow to dippos
+            armmove(armdippos, 1);
+            elbowmove(elbowdippos, 1);
+            break;
+        case 79: //"O"
+            //Move arm/elbow to ticklepos
+            armmove(armticklepos, 1);
+            elbowmove(elbowticklepos, 1);
+            break;
+        case 80: //"P"
+            //Move arm/elbow to feedpos
+            armmove(armfeedpos, 1);
+            elbowmove(elbowfeedpos, 1);
+            break;
+        case 81: //"Q"
+            //Print SWdetect value
+            wait(0.1);
+            swvalue = vswdetect.read();
+            acucomms.printf("\rVSWDETECT: %5.3f", swvalue);
+            break;
+        case 82: //"R"
+            //multiple calibrations to see variation
+            acucomms.printf("\r\nBee holder: %4u", getserialno());
+            for (int i=0; i<40; i++) {
+                acucomms.printf("\r\nN%3u C=%5.3f", i+1, calibrate(5));
+                wait(15);
+            }
+            acucomms.printf("\r\nDone");
+            break;
+        case 83: //"S"
+            //Toggle air switcher
+            airswitcher = !airswitcher;
+            if (airswitcher) {
+                acucomms.printf("\n\rAirswitcher on");
+            }
+            else {
+                acucomms.printf("\n\rAirswitcher off");
+            }
+            break;
+        case 84: //"T"
+            //set date and time on RTC
+            setdatetime();
+            break;
+        default: //All other characters
+            //Do nothing
+            break;
+        }
+        if (comchar != 88) comchar=0;
+    }
+    acucomms.printf("\n\rSession closed");
+    //Close logfile
+    fprintf(logfile, "session closed");
+    fclose(logfile);                                                //close logfile for reading    
+}
diff -r 000000000000 -r 0993f4cf5312 mbed.bld
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mbed.bld	Mon Jul 25 11:52:02 2011 +0000
@@ -0,0 +1,1 @@
+http://mbed.org/users/mbed_official/code/mbed/builds/63bcd7ba4912