Merge branch 'Hrishi'

Author: dilawar

.gitignore

@@ -121,3 +121,4 @@ eye-Blink_Conditioning.xcodeproj/project.xcworkspace/contents.xcworkspacedata
 eye-Blink_Conditioning.xcodeproj/project.pbxproj
 *.o
 
+CAD/KiCAD/AnimalBehaviour.kicad_pcb-bak

src/RotaryEncoder.h Arduino/RotaryEncoder.hsrc/RotaryEncoder.h renamed to Arduino/RotaryEncoder.h

@@ -0,0 +1,118 @@
+/*
+ *    Description:  Shock protocol. 
+ *        Author :  Upinder Bhalla. See attached file on issue #44.
+ *     Maintainer:  Dilawar Singh (), dilawars@ncbs.res.in
+ *   Organization:  NCBS Bangalore
+ *
+ */
+
+#ifndef SHOCKER_H
+#define SHOCKER_H
+
+#include "TimerOne/TimerOne.h"
+
+void enableReadingShockPad();
+void disableReadingShockPad();
+
+int NUM_SAMPLES        = 100;
+volatile size_t idx           = 0;
+
+// Do analog sampling only 1 in 10 times, for a freq of of 100 Hz.
+int SAMPLING_DIVIDER   = 10;
+int STIM_INTERVAL      = 150;
+int NUM_LOOP_RESET     = 50;
+
+// Minimum reading for foot touch to allow stimulus to go ahead.
+int TOUCH_THRESHOLD    = 50;
+int numLoops           = 0;
+volatile int shock_pin_readout  = 0;
+
+
+// To save the adc status.
+byte adc_;
+
+// Enable disable STIM isolator.
+void enableInputToStimIsolator()
+{
+    digitalWrite(SHOCK_STIM_ISOLATER_PIN, HIGH);
+}
+
+void disableInputToStimIsolator()
+{
+    digitalWrite(SHOCK_STIM_ISOLATER_PIN, LOW);
+}
+
+// Voltage across shock pad should be 5v.
+void disableReadingShockPad()
+{
+    // First switch off each pin.
+    digitalWrite( SHOCK_RELAY_PIN_CHAN_12, HIGH );
+    digitalWrite( SHOCK_RELAY_PIN_CHAN_34, LOW );
+    shock_pin_readout = 0;
+}
+
+void enableReadingShockPad()
+{
+    // The order is very important here. Don't switch them ON at the same time.
+    // First switch OFF the high voltage input and wait for some time. then
+    // switch ON the low voltage input
+    digitalWrite( SHOCK_RELAY_PIN_CHAN_34, HIGH );
+    digitalWrite( SHOCK_RELAY_PIN_CHAN_12, LOW );
+}
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis  Shock monitor is being a called every 100us (0.1ms or 10k). Use
+ * this to generate a tone on SHOCK_PWM_PIN.
+ */
+/* ----------------------------------------------------------------------------*/
+void shockMonitor() 
+{
+    // Generate 5K tone.
+    if( HIGH == digitalRead( SHOCK_PWM_PIN ))
+        digitalWrite(SHOCK_PWM_PIN, LOW);
+    else
+        digitalWrite(SHOCK_PWM_PIN, HIGH);
+
+    idx++;
+
+    // Read very 10 ms.
+    if( idx == 10)
+    {
+        noInterrupts();
+        shock_pin_readout = analogRead( SHOCK_PAD_READOUT_PIN );
+        interrupts();  // enable interrupts again. We are done reading values.
+        idx = 0;
+    }
+}
+
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis  ISR.
+ *
+ * THIS TIMER IS 8 bit.
+ *
+ * NOTE: Timer1 controlls pin 5. This PIN acts as a fast switch: switching
+ *       between stimulus delivery (when available) and reading value from
+ *       SHOCK pad. When reading values from SHOCK_VALUE, a 5V 
+ *
+ *       TIMER0 is used by millis(), delays() etc. Better I do not touch it.
+ *       TIMER2 is used by tone(). You can't use it here.
+ *
+ *       TIMER1 is used which is 16 bits.
+ */
+/* ----------------------------------------------------------------------------*/
+
+void configureShockingTimer() 
+{
+    Serial.println("[INFO] Configuring ShockingTimer --- ");
+    // Timer1.initialize(microseconds);
+    // Begin using the timer. This function must be called first. "microseconds" 
+    // is the period of time the timer takes.
+    Timer1.initialize(100); 
+    Timer1.attachInterrupt( shockMonitor );
+}
+
+
+#endif /* end of include guard: SHOCKER_H */

Arduino/Shocker.h

@@ -0,0 +1,33 @@
+#TimerOne Library#
+
+Paul Stoffregen's modified TimerOne.  This version provides 2 main benefits:
+
+1: Optimized inline functions - much faster for the most common usage  
+2: Support for more boards (including ATTiny85 except for the PWM functionality)
+
+http://www.pjrc.com/teensy/td_libs_TimerOne.html
+
+https://github.com/PaulStoffregen/TimerOne
+
+Original code
+
+http://playground.arduino.cc/Code/Timer1
+
+Open Source License
+
+TimerOne is free software. You can redistribute it and/or modify it under
+the terms of Creative Commons Attribution 3.0 United States License.
+To view a copy of this license, visit
+
+http://creativecommons.org/licenses/by/3.0/us/
+
+Paul Stoffregen forked this version from an early copy of TimerOne/TimerThree
+which was licensed "Creative Commons Attribution 3.0" and has maintained
+the original "CC BY 3.0 US" license terms.
+
+Other, separately developed updates to TimerOne have been released by other
+authors under the GNU GPLv2 license.  Multiple copies of this library, bearing
+the same name but distributed under different license terms, is unfortunately
+confusing.  This copy, with nearly all the code redesigned as inline functions,
+is provided under the "CC BY 3.0 US" license terms.
+

Arduino/TimerOne/README.md

@@ -0,0 +1,59 @@
+/*
+ *  Interrupt and PWM utilities for 16 bit Timer1 on ATmega168/328
+ *  Original code by Jesse Tane for http://labs.ideo.com August 2008
+ *  Modified March 2009 by Jérôme Despatis and Jesse Tane for ATmega328 support
+ *  Modified June 2009 by Michael Polli and Jesse Tane to fix a bug in setPeriod() which caused the timer to stop
+ *  Modified Oct 2009 by Dan Clemens to work with timer1 of the ATMega1280 or Arduino Mega
+ *  Modified April 2012 by Paul Stoffregen
+ *  Modified again, June 2014 by Paul Stoffregen
+ *  Modified July 2017 by Stoyko Dimitrov - added support for ATTiny85 except for the PWM functionality
+ *
+ *  This is free software. You can redistribute it and/or modify it under
+ *  the terms of Creative Commons Attribution 3.0 United States License. 
+ *  To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/us/ 
+ *  or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.
+ *
+ */
+
+#include "TimerOne.h"
+
+TimerOne Timer1;              // preinstatiate
+
+unsigned short TimerOne::pwmPeriod = 0;
+unsigned char TimerOne::clockSelectBits = 0;
+void (*TimerOne::isrCallback)() = TimerOne::isrDefaultUnused;
+
+// interrupt service routine that wraps a user defined function supplied by attachInterrupt
+#if defined (__AVR_ATtiny85__)
+ISR(TIMER1_COMPA_vect)
+{
+  Timer1.isrCallback();
+}
+#elif defined(__AVR__)
+ISR(TIMER1_OVF_vect)
+{
+  Timer1.isrCallback();
+}
+#elif defined(__arm__) && defined(TEENSYDUINO) && (defined(KINETISK) || defined(KINETISL))
+void ftm1_isr(void)
+{
+  uint32_t sc = FTM1_SC;
+  #ifdef KINETISL
+  if (sc & 0x80) FTM1_SC = sc;
+  #else
+  if (sc & 0x80) FTM1_SC = sc & 0x7F;
+  #endif
+  Timer1.isrCallback();
+}
+#elif defined(__arm__) && defined(TEENSYDUINO) && (defined(__IMXRT1052__) || defined(__IMXRT1062__))
+void TimerOne::isr(void)
+{
+  FLEXPWM1_SM3STS = FLEXPWM_SMSTS_RF;
+  Timer1.isrCallback();
+}
+
+#endif
+
+void TimerOne::isrDefaultUnused()
+{
+}