======= Synchronization =======
This section describes how synchronization is achieved.
  * TDT data is stored as a continuous data (starting from start of recording) 
  * behavioral data is stored per trial (starting from first trial)
Synchronization is enabled by sending state and trial information from monkeypsych to TDT ([[ephys_pipeline:2_synchronization#Synchronization during recording|Online communication]]).
Both state and trial information is sent through the same 8 pins, a little trick allows using the same channel for both purposes ([[ephys_pipeline:2_synchronization#Resulting 8 pin state signal|State signal]] ).
For combining both, we first convert TDT data to trial format (function TDT_trial_struct.m) preferentially using epocs store (Tnum and SVal) information. 
There is a flag in TDT_trial_struct for using the continous state information stream (stream_state_info), but it is permanently turned off, as the epoc information is already extracted from the continuous state information within the TDT circuit (see [[ephys_pipeline:2_synchronization#Internal TDT RCO|RCO]] )
Finally, when fitting TDT data into a trial structure, certain timing conventions have proved useful: [[ephys_pipeline:2_synchronization#Snippet and Stream synchronization in the combined trial structure
|Trial structure timing]]
====== Synchronization during recording ======
{{:ephys_pipeline:monkeypsych_dev_to_tdt_snychronization.png|}}

Note that pins are only switched either to send trial information or after a state change (AND after the flip happened!)
The idea is that both trial information and state information can be sent via the same channel.
Details are described below.
====== Resulting 8 pin state signal ======

{{:ephys_pipeline:digital_communication_monkeypsych_to_tdt.png |}}

Values of 252 to 255 are preserved for indicating start of trial/state information and in-between trial information stoppers:
  * 252: indicates start of trial information
  * 254: in between trial information to define trialinfo packages
  * 253: end of trial information
  * 255: start of state information

Note that due to preserved values, a trial information package maximum value is limited. For example, to encode the date first package would be first 2 digits of the year, second package the last 2 digits of the year, third package the month and fourth package the day. That way none of the packages reaches a value of over 100.
Trial information is sent during INI (state 1), during the other states the stat value reflects the current state.

====== TDT Internal RCO ======
{{:ephys_pipeline:tdt_stored_data.png |}}

====== Snippet and Stream synchronization in the combined trial structure ======
{{:ephys_pipeline:tdt_mp_timing.png |}}

\\ Importantly, trial start reference is STATE 2 (fixation acquisition). Trial end is STATE 2 of the next trial. 
\\ Therefore, ITI between trial 1 and 2 as well as STATE 1 (initiation) of trial 2 are found at the end of trial 1. 
\\ This also means that data recorded before 1st trial's state 2 can not be stored in the trial structure and is saved in a separate variable (First_trial_INI) instead. Everything before first trials INI is discarded.