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I removed the minus sign in line 215. The sign convention for the acceleration is already defined in line 159.

Firmware/complementary_coded_rotary_switch/Rev 2.0/control.ino

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+// Firmware version 2. Release date: 01.07.2022 //This version of the firmware features a complementary-coded rotary switch.
+
+// In no respect shall DanInvents be accountable for any liabilities, claims, demands, damages or suits resulting from the use of
+// the flight controller and/or this software. By using this software, you assume all risks associated with this product and
+// its associated features. While the circuitry and software have been tested, they should be considered experimental and handled
+// with caution.
+
+// Before uploading this code make sure that you have downloaded the latest ADXL343 (Adafruit) and MS5637 (Sparkfun) libraries.
+// You will also need the Circular Buffer library by Roberto Lo Giacco.
+// Thanks to Adafruit, Sparkfun and Roberto for the open source libraries and also to Homemade Multibody Dynamics for a guide into how to log data fast.
+// Thanks to MartinMcC for showing how to use a rotary encoder with a microcontroller.
+// Special thanks to Barun Basnet for the exceptional work on Kalman filters.
+// Special thanks to Earle Philhower for providing the support that allows using the Arduino libraries and IDE with the RP2040.
+
+// Firmware improvements over the previous version:
+
+// Changed the sign of the longitudinal acceleration. Now positive acceleration is pointing downwards and negative upwards.
+// Changed the way that launch is detected. Now the altitude must be greater than 10 m and the acceleration higher than 2 gs for over 100 ms.
+// Modified the Kalman filter parameters. Now the filtered data closely follows the measured values but featuring lower noise. This guarantees accurate apogee detection.
+// Modified the frequency at which the flight computer beeps, now it beeps less frequently before launch.
+// Now the flight computer goes silent once launch is detected. After 5 minutes, the flight computer beeps and flashes the altitude.
+// For example, 5 beeps/flashes followed by 7 beeps/flashes means 57 meters.
+// Now the flight computer can rotate a servo 180 degrees (not yet tested).
+// When set to a possition between 
+
+#include <Wire.h>
+#include "SparkFun_MS5637_Arduino_Library.h"
+#include <Adafruit_Sensor.h>
+#include <Adafruit_ADXL343.h>
+#include <SPI.h>
+#include <SD.h>
+#include <Servo.h>
+#include <EEPROM.h>
+#include <CircularBuffer.h>
+#include "pico/stdlib.h"
+
+CircularBuffer <float,100> FilteredAltitudes;
+CircularBuffer <float,100> altitudes;
+CircularBuffer <float,100> accelerations;
+CircularBuffer <long,100> times;
+
+//Initialization of Kalman Variables
+float R = 0.3; //R = measurement noise covariance. Larger R means large measurement uncertainty
+float Q = 0.3*1e-2;  //Q = process noise covariance. Larger Q means larger estimation uncertainty. Thus increasing Q corrects more
+double Xpe0;  // Xpe0 = prior estimation of signal X at time t=0 (current state)
+double Xe1;  //Xe1 = estimation of X at time t=1 (previous state)
+double Ppe0;  //Ppe0 = prior estimation of "error covariance" at t=0
+double P1,P0; //P1 = error covariance at t=1, P0 = error covariance at t=0
+double K, Xe0, Z; //K = Kalman gain, Xe0 = estimation of signal at t=0, Z = measured signal at t=0
+
+//Physical magnitudes
+float altold; //Baseline pressure
+int altMax; //Rounded maximum altitude
+int altMaxDig[4] = {}; //Max altitude digits
+int rmnd; //Dummy variable remainder
+int dvsr; //Dummy variable for beeping/flasing the altitude
+float temp;
+float currentPressure;
+float altitudeDelta;
+float altThreshold = 10.0; //Altitude threshold for launchd detection in meters
+float accelThreshold = 2.0; //Acceleration threshold for launch detection in gs.
+float filteredAltitudeDelta;
+float rocketAccel;
+float startingPressure = 0.0;
+
+//Definition of time and auxiliary integers
+int tconfig, n, q, p = 0, r = 0;
+int deltat; //Time step of every loop iteration
+long int t1; //Time variables
+long int t4, tout = 300000; //Here tout is the timeout variable tout = 300000 equals 5 min of data logging time
+
+/* Assign a unique ID to this sensor at the same time */
+Adafruit_ADXL343 accel = Adafruit_ADXL343(12345, &Wire1);
+
+//Config. rotary switch. This configuration is for the real-coded rotary switch
+byte switchPins[4] = {15, 13, 14, 16}; //Digital pins assigned to the rotary switch
+byte rotValue = B0000; // Variable for printing value over serial debug
+byte switchPos; // Variable for storing the current switch possition
+byte previousValue; //Variable for storing the previous switch possition
+
+//Boolean variables defining the state of the program
+bool initVar = true;
+bool launchCondition1 = false;
+bool launchCondition2 = false;
+bool deploy = false;
+bool automatic = false;
+bool timer = false;
+bool overtime = false;
+bool piezoEnable = true;
+
+//LEDs
+int batLED = 2; //Battery indicator LED
+int statusLED = 26; //Status LED
+
+//Servos
+int servo1pin = 28;
+int servo2pin = 27;
+
+//Piezo
+int piezo = 12;
+
+MS5637 barometricSensor; //Creates a barometricSensor object
+File dataFile; //Creates a dataFile object
+Servo servo1; //Creates a servo1 object
+Servo servo2; //Creates a servo2 object
+
+void setup() {
+  //Serial.begin(9600); //For debugging purposes only
+  EEPROM.begin(512); //Emulates EEPROM by allocating 512 kB from the flash memory
+
+  //Declaration of the I2C pins
+  Wire1.setSDA(10);
+  Wire1.setSCL(11);
+
+  //Declaration of the SPI pins
+  SPI.setRX(20);
+  SPI.setTX(19);
+  SPI.setSCK(18);
+  SPI.setCS(17);
+
+  //Declaration of the pins for the battery indicator, and status LED as well as the pin for the buzzer
+  pinMode(batLED, OUTPUT); //Low battery LED
+  pinMode(statusLED, OUTPUT); //Status LED
+  pinMode(piezo, OUTPUT); //Piezo buzzer
+
+  //Piezo buzzer PWM settings
+  analogWriteFreq(4000); //Set the piezo frequency to 4kHz
+  analogWriteRange(100); //Set the dynamic range of the piezo
+   
+  for (int i = 0; i < 4; i = i + 1){
+     pinMode(switchPins[i], INPUT_PULLUP);
+  }
+
+  barometricSensor.begin(Wire1);
+  barometricSensor.setResolution(ms5637_resolution_osr_1024);
+  
+  //Take 16 readings and average them
+  startingPressure = 0.0;
+  for (int x = 0 ; x < 16 ; x++)
+    startingPressure += barometricSensor.getPressure();
+  startingPressure /= (float)16;
+
+  accel.begin();
+  accel.setRange(ADXL343_RANGE_16_G);
+  accel.setDataRate(ADXL343_DATARATE_400_HZ);
+  switchStartup();
+  SDstartup();  //Initialize the SD card  
+  preLaunch(); //Here I store the first second of data into the circular buffers
+}
+
+void loop() {
+  batteryStatus(); //Check the battery level
+  
+  if (overtime == false){
+    currentPressure = barometricSensor.getPressure();
+    temp = barometricSensor.getTemperature();
+    sensors_event_t event;
+    accel.getEvent(&event);
+    rocketAccel = -((event.acceleration.y/9.81)-(event.acceleration.x/9.81))/sqrt(2);
+    altitudeDelta = barometricSensor.altitudeChange(currentPressure, startingPressure);
+    filteredAltitudeDelta = kalmanFilter(altitudeDelta);
+    
+
+    if (altitudeDelta > altThreshold && launchCondition1 == false){ //Threshold condition set to 10 m
+      launchCondition1 = true;
+    }
+    
+    if (rocketAccel > accelThreshold && launchCondition2 == false){
+      q++;
+      if (q > 10){ //launcCondition2 stablishes the requirement that to detect launch there should be at least an acceleration of 2g for 100 ms
+        launchCondition2 = true;
+      }
+    }
+
+    else if (rocketAccel < accelThreshold && launchCondition2 == false){
+      q = 0;
+    }
+
+    if (initVar == true){ //Store data to the circular buffer
+      accelerations.push(rocketAccel);
+      altitudes.push(altitudeDelta);
+      FilteredAltitudes.push(filteredAltitudeDelta);
+      times.push(millis()-t4); //Circular buffer for time
+
+      if (launchCondition1 == true && launchCondition2 == true){
+        initVar = false;
+          
+        for (int i = 0; i<=99; i++){ //Saving the buffer allows me to store the data measured before launch.
+         dataFile.print(times[i]-times[0]); //Here times[0] sets the time zero for the time variable
+         dataFile.print(',');
+         dataFile.print(altitudes.shift());
+         dataFile.print(',');
+         dataFile.print(FilteredAltitudes.shift());
+         dataFile.print(',');
+         dataFile.print(accelerations.shift());
+         dataFile.print(',');
+         dataFile.print(event.acceleration.z/9.81);
+         dataFile.print(',');
+         dataFile.println(temp, 1);
+        }
+          
+         dataFile.flush(); //Store data of the 908 ms before launch
+       }
+     }      
+
+    else if (initVar == false){
+      t1 = millis() - t4 - times[0];
+      recovery();  
+      dataFile.print(t1);
+      dataFile.print(',');
+      dataFile.print(altitudeDelta);
+      dataFile.print(',');
+      dataFile.print(filteredAltitudeDelta);
+      dataFile.print(',');
+      dataFile.print(rocketAccel);
+      dataFile.print(',');
+      dataFile.print(event.acceleration.z/9.81);
+      dataFile.print(',');
+      dataFile.println(temp, 1);
+
+      if (altitudeDelta > altold){ //Here is where I store the maximum altitude value
+        altMax = round(altitudeDelta);
+        altold = altMax;
+      }
+  
+      if (r == 200 && overtime == false){ //Here I set the rate at which I send data to the uSD card
+        r = 0;
+        dataFile.flush();
+       }
+       r++;
+       
+    
+      if (t1 >= tout){
+        overtime = true;
+        dataFile.flush();
+        dataFile.close(); //After timeout flush the data to the microSD card and close the file
+      }
+    }
+ }
+ beepnblink();
+}

Firmware/real_coded_rotary_switch/Rev 2.0/control.ino

@@ -212,7 +212,7 @@ void loop() {
       dataFile.print(',');
       dataFile.print(filteredAltitudeDelta);
       dataFile.print(',');
-      dataFile.print(-rocketAccel);
+      dataFile.print(rocketAccel);
       dataFile.print(',');
       dataFile.print(event.acceleration.z/9.81);
       dataFile.print(',');