Keisuke Sehara / Mbed 2 deprecated STM32_Whisking

fast-feedback virtual target task code on STM Nucleo

Dependencies:   mbed

trial.h@17:0b241aa1f5b6, 2018-07-01 (annotated)

Committer:
gwappa
Date:
Sun Jul 01 13:00:43 2018 +0000
Revision:
17:0b241aa1f5b6
Parent:
16:33c17c62840e
Child:
19:50663f8815b8
change the criterion of a catch trial

Who changed what in which revision?

UserRevisionLine numberNew contents of line
gwappa 2:0c241937eabd 1 #ifndef TRIAL_H_
gwappa 2:0c241937eabd 2 #define TRIAL_H_
gwappa 2:0c241937eabd 3
gwappa 2:0c241937eabd 4 #include "task.h"
gwappa 3:991c6d5ce19d 5 #include "arraylist.h"
gwappa 13:8ea85a33e37a 6 #include "random.h"
gwappa 3:991c6d5ce19d 7
gwappa 3:991c6d5ce19d 8 typedef int trialtime_t;
gwappa 2:0c241937eabd 9
gwappa 2:0c241937eabd 10 namespace TrialFlags {
gwappa 2:0c241937eabd 11 // nothing
gwappa 2:0c241937eabd 12 const char Clear = 0x00;
gwappa 2:0c241937eabd 13 // flags if the auditory cue is there during the trial
gwappa 2:0c241937eabd 14 const char Cues = 0x01;
gwappa 7:6744ec9ccc25 15 // flags if any "response" is detected during the response window
gwappa 2:0c241937eabd 16 const char Responded = 0x02;
gwappa 2:0c241937eabd 17 // flags if licking event is detected during the preparatory/pre-response window
gwappa 2:0c241937eabd 18 const char Licked = 0x04;
gwappa 2:0c241937eabd 19 }
gwappa 2:0c241937eabd 20
gwappa 2:0c241937eabd 21 namespace Responses {
gwappa 2:0c241937eabd 22 const char Hit = 0x03; // cues && responded
gwappa 2:0c241937eabd 23 const char Miss = 0x01; // cues && ~responded
gwappa 2:0c241937eabd 24 const char Catch = 0x02; // ~cues && responded
gwappa 2:0c241937eabd 25 const char Reject = 0x00; // ~cues && ~responded
gwappa 2:0c241937eabd 26 const char Reset = 0x04; // invalid lick
gwappa 2:0c241937eabd 27 const char NA = 0x08; // default
gwappa 2:0c241937eabd 28 }
gwappa 2:0c241937eabd 29
gwappa 2:0c241937eabd 30 struct Trial {
gwappa 2:0c241937eabd 31 /**
gwappa 2:0c241937eabd 32 * whether the animal whisked during the cue.
gwappa 2:0c241937eabd 33 * + whether the animal waited for the cue.
gwappa 2:0c241937eabd 34 */
gwappa 2:0c241937eabd 35 char response;
gwappa 2:0c241937eabd 36 /**
gwappa 2:0c241937eabd 37 * the timestamp when the trial started.
gwappa 2:0c241937eabd 38 */
gwappa 3:991c6d5ce19d 39 trialtime_t starting;
gwappa 2:0c241937eabd 40 /**
gwappa 2:0c241937eabd 41 * the timestamp when the cue started
gwappa 2:0c241937eabd 42 */
gwappa 3:991c6d5ce19d 43 trialtime_t cuestarting;
gwappa 2:0c241937eabd 44 /**
gwappa 2:0c241937eabd 45 * the total waiting period for the animal during this trial before the cue.
gwappa 2:0c241937eabd 46 */
gwappa 2:0c241937eabd 47 unsigned long waiting; // used for calculation of waiting period
gwappa 2:0c241937eabd 48 /**
gwappa 2:0c241937eabd 49 * the duration of the delay period for this trial.
gwappa 2:0c241937eabd 50 */
gwappa 2:0c241937eabd 51 uint16_t delay_dur_ms;
gwappa 2:0c241937eabd 52
gwappa 13:8ea85a33e37a 53 // (passive) visual cue-related params
gwappa 16:33c17c62840e 54 uint16_t vis_onset_us;
gwappa 16:33c17c62840e 55 uint16_t vis_dur_us;
gwappa 13:8ea85a33e37a 56
gwappa 11:897ecd5413e0 57 uint64_t aud_ticker_cycle;
gwappa 11:897ecd5413e0 58
gwappa 17:0b241aa1f5b6 59 /**
gwappa 17:0b241aa1f5b6 60 * a buffer for recording licking events during the trial.
gwappa 17:0b241aa1f5b6 61 */
gwappa 3:991c6d5ce19d 62 ArrayList<trialtime_t> licking_events;
gwappa 17:0b241aa1f5b6 63
gwappa 17:0b241aa1f5b6 64 /**
gwappa 17:0b241aa1f5b6 65 * a buffer for recording whisking events during the trial.
gwappa 17:0b241aa1f5b6 66 */
gwappa 3:991c6d5ce19d 67 ArrayList<trialtime_t> whisking_events;
gwappa 3:991c6d5ce19d 68
gwappa 17:0b241aa1f5b6 69 /**
gwappa 17:0b241aa1f5b6 70 * initialize the trial parameters according to the given Task parameter set.
gwappa 17:0b241aa1f5b6 71 * typically called from one of the automaton states.
gwappa 17:0b241aa1f5b6 72 */
gwappa 2:0c241937eabd 73 void reset(const Task& task);
gwappa 2:0c241937eabd 74
gwappa 13:8ea85a33e37a 75 /**
gwappa 13:8ea85a33e37a 76 * a helper function to assign onset & duration randomly for the (passive) visual cue.
gwappa 13:8ea85a33e37a 77 *
gwappa 13:8ea85a33e37a 78 * the `onset` will distribute exponentially from `0` to `auddur - respdur - mindur`.
gwappa 13:8ea85a33e37a 79 * the `duration` will distribute uniformly from `mindur` to `phasedur - onset`.
gwappa 13:8ea85a33e37a 80 */
gwappa 13:8ea85a33e37a 81 void assignRandomStim(const Task& task);
gwappa 13:8ea85a33e37a 82
gwappa 17:0b241aa1f5b6 83 /**
gwappa 17:0b241aa1f5b6 84 * a callback mechanism for marking (timestamping) the start of the trial.
gwappa 17:0b241aa1f5b6 85 * called from one of the automaton states.
gwappa 17:0b241aa1f5b6 86 */
gwappa 11:897ecd5413e0 87 void markTrialStart();
gwappa 17:0b241aa1f5b6 88
gwappa 17:0b241aa1f5b6 89 /**
gwappa 17:0b241aa1f5b6 90 * a callback mechanism for marking (timestamping) the end of the waiting period of the trial.
gwappa 17:0b241aa1f5b6 91 * called from one of the automaton states.
gwappa 17:0b241aa1f5b6 92 */
gwappa 11:897ecd5413e0 93 void markEndOfWait();
gwappa 17:0b241aa1f5b6 94
gwappa 17:0b241aa1f5b6 95 /**
gwappa 17:0b241aa1f5b6 96 * a callback mechanism for marking (timestamping) the end of the trial.
gwappa 17:0b241aa1f5b6 97 * called from one of the automaton states.
gwappa 17:0b241aa1f5b6 98 */
gwappa 11:897ecd5413e0 99 void markTrialEnd();
gwappa 11:897ecd5413e0 100
gwappa 17:0b241aa1f5b6 101 /**
gwappa 17:0b241aa1f5b6 102 * output the result of a trial into a serial port through the IO mechanism.
gwappa 17:0b241aa1f5b6 103 * typically called from one of the automaton states.
gwappa 17:0b241aa1f5b6 104 */
gwappa 2:0c241937eabd 105 void writeToSerial();
gwappa 2:0c241937eabd 106 };
gwappa 2:0c241937eabd 107
gwappa 2:0c241937eabd 108 #endif