Reading data only when present - matlab

I'm trying to read the data from the COM3 port.
I'm using this code:
in = fscanf(s);
if(in == 'A')
fclose(s);
break;
end
The problem is that when no data is sent to the com3 port, the fscanf() will wait for a certain time interval and then give a timeout.
Is there a way to read data only when it is present?

Read only when data present
You can read out the BytesAvailable-property of the serial object s to know how many bytes are in the buffer ready to be read:
bytes = get(s,'BytesAvailable'); % using getter-function
bytes = s.BytesAvailable; % using object-oriented-addressing
Then you can check the value of bytes to match your criteria. Assuming a char is 1 byte, then you can check for this easily before reading the buffer.
if (bytes >= 1)
in = fscanf(s);
% do the handling of 'in' here
end
Minimize the time to wait
You can manually set the Timeout-property of the serial object s to a lower value to continue execution earlier as the default timeout.
set(s,'Timeout',1); % sets timeout to 1 second (default is 10 seconds)
Most likely you will get the following warning:
Unsuccessful read: A timeout occurred before the Terminator was
reached..
It can be suppressed by executing the following command before fscanf.
warning('off','MATLAB:serial:fscanf:unsuccessfulRead');
Here is an example:
s = serial('COM3');
set(s,'Timeout',1); % sets timeout to 1 second (default is 10 seconds)
fopen(s);
warning('off','MATLAB:serial:fscanf:unsuccessfulRead');
in = fscanf(s);
warning('on','MATLAB:serial:fscanf:unsuccessfulRead');
if(in == 'A')
fclose(s);
break;
end

Related

How do I synchronize clocks on two Raspberry Pi Picos?

I'm sending bits as LED blinks from one Pi Pico, and using another Pico to receive voltage from a photodiode and read the bits.
When sending/receiving from the same PiPico, it works accurately at 60us a bit. However, when sending from one pico and receiving from a second pico, I can only send/receive bits accurately at 0.1s a bit. If I move to sending/receiving at 0.01s, I start losing information. This leads me to believe my issue is with the clocks or sampling rates on the two pipicos, that they are slightly different.
Is there a way to synchronize two pipico clocks using Thonny/Micropython?
Code for Pico #1 sending blinks/bits:
led=Pin(13,Pin.OUT) #Led to blink
SaqVoltage = machine.ADC(28) #receive an input signal, when over a certain voltage, send the time using bits
#Ommitted code here to grab first low voltage values from SaqVoltage signal and use to determine if there is a high voltage received, when high voltage is received, send "hi" in led bits
#More omitted calibration code here for led/photodiode
hi = "0110100001101001"
while True:
SaqVoltage_value = SaqVoltage.read_u16()*3.3 / 65536 #read input signal to see if high voltage is sent
finalBitString = ""
if SaqVoltage_value > saQCutOff: #high voltage found, send "hi" sequence
finalBitString = #hi plus some start/stop sequences
for i in range (0, len(finalBitString)):
if finalBitString[i]=="1":
led(1)
elif finalBitString[i]=="0":
led(0)
utime.sleep(.01)
Code for Pico#2 receiving bits:
SaqDiode = machine.ADC(28) #read photodiode
#ommitted code here to calibrate leds/photodiodes
startSeqSaq = []
wordBits=[]
while True:
utime.sleep(.01) #sample diode every 0.01 seconds
SaqDiode_value = SaqDiode.read_u16()*3.3 / 65536
if (saqDiodeHi - saqCutOff <= SaqDiode_value): #read saq diode and determine 1 or 0
bit=1
elif (SaqDiode_value <= saqDiodeLo + saqCutOff):
bit=0
if len(startSeqSaq)==10: #record last 10 received bits to check if start sequence
startSeqSaq.pop(0)
startSeqSaq.append(bit)
elif len(startSeqSaq)<10:
startSeqSaq.append(bit)
if startSeqSaq == startSeq: #found start sequence, start reading bits
while True:
utime.sleep(.01)
SaqDiode_value = SaqDiode.read_u16()*3.3 / 65536
if (saqDiodeHi - saqCutOff <= SaqDiode_value):
bit=1
wordBits.append(bit)
elif (SaqDiode_value < saqDiodeLo + saqCutOff):
bit=0
wordBits.append(bit)
if len(wordBits)>10: #check for stop sequence
last14=wordBits[-10:]
else:
last14 = []
if last14==endSeq:
char = frombits(wordBits[:-10])
wordBits=[]
print("Function Generator Reset Signal Time in ms from Start: ", char)
break

Saving synchronised 7T fMRI Triggers received via USB connected NNL SyncBox, on every TR and Task Response Keypress (PsychoPy)

I would like to get synchronised timings and number of triggers for each single pulse sent by the 7T MRI scanner together with each single SPACEBAR keypress as a participant’s response when particular letters (A, B, C, X, Y) are presented on the screen, also the stimulus start time with each corresponding trigger.
So far I have added a “Waiting for scanner” routine where I get the first pulse via USB connected NNL Synbox saved in the .csv data file but I want to save each single pulse (TR) and timings. Triggers are automatically emulated as letter ‘s’ sent by the NNL Synbox.
# Code component: Creat routine "Wait for Scanner"
text_wait = visual.TextStim(win=win, name='text_wait',
text='Waiting for scanner...',
font='Arial',
pos=(0, 0), height=0.8, wrapWidth=None, ori=0,
color='white', colorSpace='rgb', opacity=1,
languageStyle='LTR',
depth=0.0);
#Set first MR Trigger
mr_trigger_number = [] # list for triggers
mr_trigger_time = [] # list for time of each trigger
ScannerKeyboard = keyboard.Keyboard() # set keyboard
count_mr_trigger = 0 # counts amount of MR scanner trigger, starts with zero
start_trigger = ScannerKeyboard.getKeys(keyList=['s'], waitRelease = False) # experiment starts with MR Scanner "s"
# Draw waiting Screen until "s" is sent from NNL Syncbox
while len(start_trigger) == 0: # if no trigger was sent show:
text_wait.draw() # Text "Waiting for scanner"
win.flip()
start_trigger = ScannerKeyboard.getKeys(keyList=['s'], waitRelease = False) # show text_wait until one "s" was received
# Get timing information and store trigger number
onset = core.getTime() # get Onset time of trigger
count_mr_trigger = count_mr_trigger + 1 # count MR Scanner trigger, add "1!
# Save time and number of MR Trigger
thisExp.addData('MR_trigger_time',onset) # save trigger time of onset
thisExp.addData('MR_trigger_number',count_mr_trigger)
And also I used the following code component in > Each Frame tab of 2 trials conditions to save the stimuli onset timings when a pulse 's' is received. This works fine but stimulus start time > stimulus_start_time = globalClock.getTime() - mr_trigger_time is saved based on first pulse only as I am unable to save each pulse timings.
#save stimulus onset time for two types of trial conditions
if trials.thisN == 0 and frameN == 0:
loop_start_time = globalClock.getTime() - mr_trigger_time
elif frameN == 1:
stimulus_start_time = globalClock.getTime() - mr_trigger_time
# store the data:
thisExp.addData('stimulus_start_time', stimulus_start_time)
if trials_2.thisN == 0 and frameN == 0:
loop_start_time = globalClock.getTime() - mr_trigger_time
elif frameN == 1:
stimulus_start_time = globalClock.getTime() - mr_trigger_time
# store the data:
thisExp.addData('stimulus_start_time', stimulus_start_time)
However, I want to record and save timings of each trigger pulse when a SPACEBAR response is pressed on a target letter (stimulus) by a participant, to compare the timings with accuracy and reaction times of the task with each corresponding trigger timings.
I would really appreciate your valuable suggestions on how to work around this, as I am quite new to the PsychoPy. I also posted to the PsychoPy forum but haven't got any update so far.
Thanks in advance!

Issue sending/receiving data over serial connection using MATLAB

I recently connected a reactor control tower through a serial 'COMMS' port to my computer (serial to USB). It seems to create a connection on the COM4 port (as indicated on the control panel 'devices and printers' section). However, it always gives me the following message when i try to 'fwrite(s)' or 'fscanf(s)'.
Warning: Unsuccessful read: The specified amount of data was not returned within the Timeout period..
%My COM4
s = serial('COM4');
s.BaudRate = 9600;
s.DataBits = 8;
s.Parity ='none';
s.StopBits = 1;
s.FlowControl='none';
s.Terminator = ';';
s.ByteOrder = 'LittleEndian';
s.ReadAsyncMode = 'manual';
% Building write message.
devID = '02'; % device ID
cmd = 'S'; % command read or write; S for write
readM = cell(961,3);% Read at most 961-by-3 values filling a 961–by–3 matrix in column order
strF = num2str(i);
strF = '11'; %pH parameter
strP = '15'; %pH set point
val = '006.8'; %pH set value
msg_ = strcat('!', devID, cmd, strF, strP, val);%output the string
chksum = dec2hex(mod(sum(msg_),256)); %conversion to hexdec
msg = strcat(msg_,':', char(chksum), ';');
fopen(s); %connects s to the device using fopen , writes and reads text data
fwrite(s, uint8(msg)); %writes the binary data/ Convert to 8-bit unsigned integer (unit8) to the instrument connected to s.
reply=fscanf(s); %reads ASCII data from the device connected to the serial port object and returns it to reply, for binary data use fread
fclose(s); %Disconnect s from the scope, and remove s from memory and the workspace.
This leads me to believe that the device is connected but is not sending or receiving information and I am unsure as to how I can configure this or even really check if there is communication occurring between the tower and my computer.

Read UART transmision Input buffer in Matlab

I'm trying to make a serial communication between two ESP8266 Wifi chips.
To start, I tried sending a sample data 10 times in a for loop. Here is the code:
Transmiter:
for Packets = 1 : 10
SendData(client,Data(Packets));
end
Receiver:
Packets = 1
while(1)
Data(Packets) = ReceiveData(Server);
Packets = Packets + 1;
if (packets == 10)
break
end
end
it works good. The problem is when I want to send data with some delays, the transmitter should connect to receiver again and the server (receiver) receives some data indicating that connection is made again.
The received Buffer should be:
+IPD,0,1024:ùüþþþýýþþÿÿûûýþýûúþÿúóýÿþþþþþýúøûýþ...
but after reconnecting the received Buffer is:
0,CLOSED %Receiver Prompt, disconnected from Transmiter
0,CONNECT %Receiver Prompt,connected to Transmiter
+IPD,0,1024:ùüþþþýýþþÿÿûûýþýûúþÿúóýÿþþþþþýúøûýþ...
The remaining part of data will be read in next packet and same for next packets.
what should I do to receive just the data?
The send and receive functions:
function ReceivedBuffer = ReceiveData(SerialPort)
ReceivedBuffer = fread(server,1038); %Size data = 1038 Bytes
end
function SendData(SerialPort,Data)
fwrite(SerialPort,Data);
end

Uploading sketch in Arduino

I am working on making an interface between MATLAB and Arduino. In other words, I want to send some data from MATLAB to Arduino. I have written programs both in MATLAB and the Arduino IDE.
MATLAB program:
c = 1;
if (c ~= 0 )
f = 1;
else
disp('vhxhjf');
end
disp(f)
arduino=serial('COM5','BaudRate',9600); % create serial communication object on port COM4
fopen(arduino); % initiate arduino communication
while f
fprintf(arduino,'%s',char(f)); % send answer variable content to arduino
end
fclose(arduino); % end communication with arduino
Code for Arduino:
int ledPin = 13;
int matlabData ;
void setup() {
pinMode(13,OUTPUT);
Serial.begin(9600);
// turn the LED on when we're done
// digitalWrite(13, HIGH);
}
void loop() {
if(Serial.available() > 0 ) {
matlabData = Serial.read();
if ( matlabData != 0) {
digitalWrite(13, HIGH);
delay(1000);
digitalWrite(13,LOW);
delay(1000);
}
else
digitalWrite(13,LOW);
}
}
The problem is whenever I am uploading the sketch , this error is being thrown regularly in arduino ide:
avrdude: ser_open(): can't open device "\\.\COM5": The system cannot find the file specified
It was works on the first try, but after that the above error is thrown continuosly .
Also in matlab, after the first try , the following error is thrown:
enter code here
Error using serial/fopen (line 72)
Open failed: Port: COM5 is not available. No ports are available.
Use INSTRFIND to determine if other instrument objects are connected to requested device.
Error in SP (line 65)
fopen(arduino); % initiate arduino communication
>> instrfind
Instrument Object Array
Index: Type: Status: Name:
1 serial open Serial-COM5
2 serial closed Serial-COM5
and also the command instrfind is showing that the com5 port is closed after the first try.
I have tried the solution given in this link but it is didn't work:
http://forum.arduino.cc/index.php?topic=48421.0
This usually happens when you don't close the port.
In your code, when do you close it? When is f changed so the loop exits?
According to these people, you can try to do
delete(instrfindall)
before trying to open the port or
fopen(arduino);
closeFID = onCleanup(#() fclose(arduino));
...
IMHO the second solution looks better (less destructive)
BTW: put a delay or a sleep (I don't know how this is done in ML) in the fprintf loop, otherwise you will send too many data to the poor Arduino...