From 273133f4647de44eedd19b0ee6ce107e1a30db5a Mon Sep 17 00:00:00 2001
From: Colin <44309126+cxider@users.noreply.github.com>
Date: Mon, 14 Nov 2022 17:38:13 -0600
Subject: [PATCH 1/3] Added USB Serial Logging Support to FED3 Library

Adds support for using sending data over the serial connection in the fed3 to a computer
---
 src/FED3.cpp | 132 +++++++++++++++++++++++++++++++++++++++++++++++++++
 src/FED3.h   |   6 +++
 2 files changed, 138 insertions(+)

diff --git a/src/FED3.cpp b/src/FED3.cpp
index 7251ebc..177a95e 100644
--- a/src/FED3.cpp
+++ b/src/FED3.cpp
@@ -975,8 +975,140 @@ void FED3::writeConfigFile() {
   configfile.close();
 }
 
+//Reset Experiment Variables
+void FED3::rest_vars(){
+  LeftCount = 0;
+  RightCount = 0;
+  PelletCount = 0;
+  BlockPelletCount = 0;
+  retInterval = 0;
+  leftInterval = 0;
+  rightInterval = 0;
+  leftPokeTime = 0;
+  rightPokeTime = 0;
+  pelletTime = 0;
+  lastPellet = 0;
+  unixtime = 0;
+  interPelletInterval = 0;
+}
+// Log Data to Serial Connection
+void FED3::logserial(){
+    DateTime now = rtc.now();
+
+    Serial.print(now.month());
+    Serial.print("/");
+    Serial.print(now.day());
+    Serial.print("/");
+    Serial.print(now.year());
+    Serial.print(" ");
+    Serial.print(now.hour());
+    Serial.print(":");
+    if (now.minute() < 10)
+      Serial.print('0');      // Trick to add leading zero for formatting
+    Serial.print(now.minute());
+    Serial.print(":");
+    if (now.second() < 10)
+      Serial.print('0');      // Trick to add leading zero for formatting
+    Serial.print(now.second());
+  Serial.print(",");
+
+  if(tempSensor == true) {
+    sensors_event_t humidity, temp;
+    aht.getEvent(&humidity, &temp);// populate temp and humidity objects with fresh data
+    Serial.print (temp.temperature);
+    Serial.print(",");
+    Serial.print (humidity.relative_humidity);
+    Serial.print(",");
+  }
+
+  Serial.print(VER); // Print library version
+  Serial.print(",");
+
+  Serial.print(sessiontype);  //print Sketch identifier
+  Serial.print(",");
+
+  Serial.print(FED); // 
+  Serial.print(",");
+
+  Serial.print(measuredvbat); // 
+  Serial.print(",");
+
+  if (Event != "Pellet"){
+    Serial.print(sqrt (-1)); // print NaN if it's not a pellet Event
+    Serial.print(",");    
+  }
+  else {
+    Serial.print(numMotorTurns+1); // Print the number of attempts to dispense a pellet
+    Serial.print(",");
+  }
+
+  Serial.print(FR);
+  Serial.print(",");
+
+  Serial.print(Event); 
+  Serial.print(",");
+
+  if (activePoke == 0)  Serial.print("Right"); //
+  if (activePoke == 1)  Serial.print("Left"); //
+  Serial.print(",");
+
+  Serial.print(LeftCount); // Print Left poke count
+  Serial.print(",");
+    
+  Serial.print(RightCount); // Print Right poke count
+  Serial.print(",");
+
+  Serial.print(PelletCount); // print Pellet counts
+  Serial.print(",");
+
+  Serial.print(BlockPelletCount); // print Block Pellet counts
+  Serial.print(",");
+
+  if (Event != "Pellet"){
+    Serial.print(sqrt (-1)); // print NaN if it's not a pellet Event
+  }
+  else if (retInterval < 60000 ) {  // only log retrieval intervals below 1 minute (FED should not record any longer than this)
+    Serial.print(retInterval/1000.000); // print interval between pellet dispensing and being taken
+  }
+  else if (retInterval >= 60000) {
+    Serial.print("Timed_out"); // print "Timed_out" if retreival interval is >60s
+  }
+  else {
+    Serial.print("Error"); // print error if value is < 0 (this shouldn't ever happen)
+  }
+  Serial.print(",");
+  
+  if ((Event != "Pellet") or (PelletCount < 2)){
+    Serial.print(sqrt (-1)); // print NaN if it's not a pellet Event
+  }
+  else {
+    Serial.print (interPelletInterval);
+  }
+  Serial.print(",");
+
+  if (Event == "Pellet"){
+    Serial.println(sqrt (-1)); // print NaN 
+  }
+
+  else if ((Event == "Left") or (Event == "LeftShort") or (Event == "LeftWithPellet") or (Event == "LeftinTimeout") or (Event == "LeftDuringDispense")) {  // 
+    Serial.println(leftInterval/1000.000); // print left poke timing
+  }
+
+  else if ((Event == "Right") or (Event == "RightShort") or (Event == "RightWithPellet") or (Event == "RightinTimeout") or (Event == "RightDuringDispense")) {  // 
+    Serial.println(rightInterval/1000.000); // print left poke timing
+  }
+  
+  else {
+    Serial.println(sqrt (-1)); // print NaN 
+  }
+  Serial.print('\0');
+}
+
 //Write to SD card
 void FED3::logdata() {
+  
+  if(SerialLogging == true) logserial(); //preform a Serial Log if enabled
+
   if (EnableSleep==true){
     digitalWrite (MOTOR_ENABLE, LOW);  //Disable motor driver and neopixel
   }
diff --git a/src/FED3.h b/src/FED3.h
index 055850d..36ba3a3 100644
--- a/src/FED3.h
+++ b/src/FED3.h
@@ -66,6 +66,7 @@ This device includes hardware and code from:
 #define STEPS 2038
 
 extern bool Left;
+extern RTC_PCF8523 rtc;
 
 class FED3 {
     // Members
@@ -143,6 +144,9 @@ class FED3 {
         void SelectMode();
         void SetDeviceNumber();
 
+        //Experement Wipe
+        void rest_vars();
+
         // Stimuli
         void ConditionedStimulus(int duration = 200);
         void Click();
@@ -204,6 +208,7 @@ class FED3 {
         unsigned long displayupdate;
         String Event = "None";   //What kind of event just happened?
         
+        
         // timing variables
         int retInterval = 0;
         int leftInterval = 0;
@@ -220,6 +225,7 @@ class FED3 {
         bool EnableSleep = true;
         void disableSleep();
         void enableSleep();
+        bool SerialLogging = false;
         bool ClassicFED3 = false;
         bool FED3Menu = false;
         bool tempSensor = false;

From e64eac9815233108251d2f285a0405af99b86927 Mon Sep 17 00:00:00 2001
From: Colin <44309126+cxider@users.noreply.github.com>
Date: Mon, 14 Nov 2022 17:41:30 -0600
Subject: [PATCH 2/3] Support for Sending Headers Over Serial

This allows you to send the headers for the log file over serial connection
---
 src/FED3.cpp | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/FED3.cpp b/src/FED3.cpp
index 177a95e..ef9a0fb 100644
--- a/src/FED3.cpp
+++ b/src/FED3.cpp
@@ -965,6 +965,19 @@ void FED3::writeHeader() {
   logfile.close();
 }
 
+void FED3::sendHeader() {
+  digitalWrite (MOTOR_ENABLE, LOW);  //Disable motor driver and neopixel
+  // Write data header to file of microSD card
+
+
+  if (tempSensor == false){
+    Serial.println("MM:DD:YYYY hh:mm:ss,Library_Version,Session_type,Device_Number,Battery_Voltage,Motor_Turns,FR,Event,Active_Poke,Left_Poke_Count,Right_Poke_Count,Pellet_Count,Block_Pellet_Count,Retrieval_Time,InterPelletInterval,Poke_Time");
+  } else {
+    Serial.println("MM:DD:YYYY hh:mm:ss,Temp,Humidity,Library_Version,Session_type,Device_Number,Battery_Voltage,Motor_Turns,FR,Event,Active_Poke,Left_Poke_Count,Right_Poke_Count,Pellet_Count,Block_Pellet_Count,Retrieval_Time,InterPelletInterval,Poke_Time");
+  }
+  Serial.print('\0');
+}
+
 //write a configfile (this contains the FED device number)
 void FED3::writeConfigFile() {
   digitalWrite (MOTOR_ENABLE, LOW);  //Disable motor driver and neopixel
@@ -1106,7 +1119,7 @@ void FED3::logserial(){
 
 //Write to SD card
 void FED3::logdata() {
-  
+
   if(SerialLogging == true) logserial(); //preform a Serial Log if enabled
 
   if (EnableSleep==true){

From 34bfc3bac93cd61b46d2ca49f0cad3708f1e8ac4 Mon Sep 17 00:00:00 2001
From: Colin <44309126+cxider@users.noreply.github.com>
Date: Tue, 15 Nov 2022 14:56:34 -0600
Subject: [PATCH 3/3] Fixed Delay Issues When Sending Headers

---
 src/FED3.cpp | 20 +++++++++++++++-----
 src/FED3.h   |  2 ++
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/FED3.cpp b/src/FED3.cpp
index ef9a0fb..8623bf8 100644
--- a/src/FED3.cpp
+++ b/src/FED3.cpp
@@ -965,17 +965,27 @@ void FED3::writeHeader() {
   logfile.close();
 }
 
-void FED3::sendHeader() {
+void FED3::sendHeaders() {
   digitalWrite (MOTOR_ENABLE, LOW);  //Disable motor driver and neopixel
   // Write data header to file of microSD card
 
 
   if (tempSensor == false){
-    Serial.println("MM:DD:YYYY hh:mm:ss,Library_Version,Session_type,Device_Number,Battery_Voltage,Motor_Turns,FR,Event,Active_Poke,Left_Poke_Count,Right_Poke_Count,Pellet_Count,Block_Pellet_Count,Retrieval_Time,InterPelletInterval,Poke_Time");
+    Serial.print("Unix Time(s),Library_Version,Session_type,Device_Number,");
+    Serial.print("Battery_Voltage,Motor_Turns,FR,Event,Active_Poke,");
+    Serial.write('\0');
+    delay(200);
+    Serial.print("Left_Poke_Count,Right_Poke_Count,Pellet_Count,");
+    Serial.print("Block_Pellet_Count,Retrieval_Time,InterPelletInterval,Poke_Time");
   } else {
-    Serial.println("MM:DD:YYYY hh:mm:ss,Temp,Humidity,Library_Version,Session_type,Device_Number,Battery_Voltage,Motor_Turns,FR,Event,Active_Poke,Left_Poke_Count,Right_Poke_Count,Pellet_Count,Block_Pellet_Count,Retrieval_Time,InterPelletInterval,Poke_Time");
-  }
-  Serial.print('\0');
+    Serial.print("Unix Time(s),Temp,Humidity,Library_Version,Session_type,Device_Number,");
+    Serial.print("Battery_Voltage,Motor_Turns,FR,Event,Active_Poke,");
+    Serial.write('\0');
+    delay(200);
+    Serial.print("Left_Poke_Count,Right_Poke_Count,Pellet_Count,");
+    Serial.print("Block_Pellet_Count,Retrieval_Time,InterPelletInterval,Poke_Time");
+  }
+  Serial.write('\0');
 }
 
 //write a configfile (this contains the FED device number)
diff --git a/src/FED3.h b/src/FED3.h
index 36ba3a3..9ee4079 100644
--- a/src/FED3.h
+++ b/src/FED3.h
@@ -88,9 +88,11 @@ class FED3 {
         File stopfile;      // Create another file object
         char filename[21];  // Array for file name data logged to named in setup
         void logdata();
+        void logserial();
         void CreateFile();
         void CreateDataFile ();
         void writeHeader();
+        void sendHeaders();
         void writeConfigFile();
         void writeFEDmode();
         void error(uint8_t errno);