Atlas Scientific Code Help

Tagged: Atlas Scientific, code, modular sensors, sensors, variables

This topic has 0 replies, 1 voice, and was last updated 2021-10-05 at 1:46 PM by Fiona.

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2021-10-05 at 1:46 PM #16040

Fiona

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Hi All,

I have everything I need to build out a system using the Mayfly and Atlas Scientific sensors, but I am stuck on how to integrate the Atlas Scientific code from menu a la carte into DRWI LTE. An electrical engineering volunteer created a shield that allows us to connect four sensors on their own electrically isolated carrier boards to the system while communicating on I2C. We are using Atlas Sci EZO circuits to include pH, electrical conductivity, dissolved oxygen, and RTD temperature.

Will I simply remove the code for the Campbell OBS 3 and Meter Hydros sensors and paste the code for each EZO circuit from menu a la carte in its place, and then change the “Creating Variable Array and Filling with Variable Objects” section and add my UUIDs? I am unsure what the lines for the Atlas sensors would look like in the variable list. Can anyone advise? I know @adamgold and @w3asa have worked with these sensors – any clues? Any help is much appreciated. Thank you! Fiona

/** =========================================================================
 * @file DRWI_LTE.ino
 * @brief Example for DRWI CitSci LTE sites.
 *
 * @author Sara Geleskie Damiano <sdamiano@stroudcenter.org>
 * @copyright (c) 2017-2020 Stroud Water Research Center (SWRC)
 *                          and the EnviroDIY Development Team
 *            This example is published under the BSD-3 license.
 *
 * Build Environment: Visual Studios Code with PlatformIO
 * Hardware Platform: EnviroDIY Mayfly Arduino Datalogger
 *
 * DISCLAIMER:
 * THIS CODE IS PROVIDED "AS IS" - NO WARRANTY IS GIVEN.
 * ======================================================================= */

// ==========================================================================
//  Defines for the Arduino IDE
//  NOTE:  These are ONLY needed to compile with the Arduino IDE.
//         If you use PlatformIO, you should set these build flags in your
//         platformio.ini
// ==========================================================================
/** Start [defines] */
#ifndef TINY_GSM_RX_BUFFER
#define TINY_GSM_RX_BUFFER 64
#endif
#ifndef TINY_GSM_YIELD_MS
#define TINY_GSM_YIELD_MS 2
#endif
/** End [defines] */

// ==========================================================================
//  Include the libraries required for any data logger
// ==========================================================================
/** Start [includes] */
// The Arduino library is needed for every Arduino program.
#include <Arduino.h>

// EnableInterrupt is used by ModularSensors for external and pin change
// interrupts and must be explicitly included in the main program.
#include <EnableInterrupt.h>

// To get all of the base classes for ModularSensors, include LoggerBase.
// NOTE:  Individual sensor definitions must be included separately.
#include <LoggerBase.h>
/** End [includes] */


// ==========================================================================
//  Data Logging Options
// ==========================================================================
/** Start [logging_options] */
// The name of this program file
const char* sketchName = "DRWI_LTE.ino";
// Logger ID, also becomes the prefix for the name of the data file on SD card
const char* LoggerID = "XXXXX";
// How frequently (in minutes) to log data
const uint8_t loggingInterval = 5;
// Your logger's timezone.
const int8_t timeZone = -5;  // Eastern Standard Time
// NOTE:  Daylight savings time will not be applied!  Please use standard time!

// Set the input and output pins for the logger
// NOTE:  Use -1 for pins that do not apply
const int32_t serialBaud = 115200;  // Baud rate for debugging
const int8_t  greenLED   = 8;       // Pin for the green LED
const int8_t  redLED     = 9;       // Pin for the red LED
const int8_t  buttonPin  = 21;      // Pin for debugging mode (ie, button pin)
const int8_t  wakePin    = A7;  // MCU interrupt/alarm pin to wake from sleep
// Set the wake pin to -1 if you do not want the main processor to sleep.
// In a SAMD system where you are using the built-in rtc, set wakePin to 1
const int8_t sdCardPwrPin   = -1;  // MCU SD card power pin
const int8_t sdCardSSPin    = 12;  // SD card chip select/slave select pin
const int8_t sensorPowerPin = 22;  // MCU pin controlling main sensor power
/** End [logging_options] */


// ==========================================================================
//  Wifi/Cellular Modem Options
// ==========================================================================
/** Start [xbee_cell_transparent] */
// For any Digi Cellular XBee's
// NOTE:  The u-blox based Digi XBee's (3G global and LTE-M global)
// are more stable used in bypass mode (below)
// The Telit based Digi XBees (LTE Cat1) can only use this mode.
#include <modems/DigiXBeeCellularTransparent.h>

// Create a reference to the serial port for the modem
HardwareSerial& modemSerial = Serial1;  // Use hardware serial if possible
const int32_t   modemBaud   = 9600;     // All XBee's use 9600 by default

// Modem Pins - Describe the physical pin connection of your modem to your board
// NOTE:  Use -1 for pins that do not apply
const int8_t modemVccPin    = -2;    // MCU pin controlling modem power
const int8_t modemStatusPin = 19;    // MCU pin used to read modem status
const bool useCTSforStatus = false;  // Flag to use the modem CTS pin for status
const int8_t modemResetPin = 20;     // MCU pin connected to modem reset pin
const int8_t modemSleepRqPin = 23;   // MCU pin for modem sleep/wake request
const int8_t modemLEDPin = redLED;   // MCU pin connected an LED to show modem
                                     // status (-1 if unconnected)

// Network connection information
const char* apn = "hologram";  // The APN for the gprs connection

DigiXBeeCellularTransparent modemXBCT(&modemSerial, modemVccPin, modemStatusPin,
                                      useCTSforStatus, modemResetPin,
                                      modemSleepRqPin, apn);
// Create an extra reference to the modem by a generic name
DigiXBeeCellularTransparent modem = modemXBCT;
/** End [xbee_cell_transparent] */


// ==========================================================================
//  Using the Processor as a Sensor
// ==========================================================================
/** Start [processor_sensor] */
#include <sensors/ProcessorStats.h>

// Create the main processor chip "sensor" - for general metadata
const char*    mcuBoardVersion = "v0.5b";
ProcessorStats mcuBoard(mcuBoardVersion);
/** End [processor_sensor] */


// ==========================================================================
//  Maxim DS3231 RTC (Real Time Clock)
// ==========================================================================
/** Start [ds3231] */
#include <sensors/MaximDS3231.h>

// Create a DS3231 sensor object
MaximDS3231 ds3231(1);
/** End [ds3231] */


#if defined MS_BUILD_TEST_ATLASDO || defined MS_BUILD_TEST_ALL_SENSORS
// ==========================================================================
//  Atlas Scientific EZO-DO Dissolved Oxygen Sensor
// ==========================================================================
/** Start [atlas_do] */
#include <sensors/AtlasScientificDO.h>

const int8_t AtlasDOPower    = sensorPowerPin;  // Power pin (-1 if unconnected)
uint8_t      AtlasDOi2c_addr = 0x61;            // Default for DO is 0x61 (97)
// All Atlas sensors have different default I2C addresses, but any of them can
// be re-addressed to any 8 bit number.  If using the default address for any
// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific DO sensor object
#ifdef MS_ATLAS_SOFTWAREWIRE
// AtlasScientificDO atlasDO(AtlasDOPower, softwareSDA, softwareSCL,
//                           AtlasDOi2c_addr);
AtlasScientificDO atlasDO(&softI2C, AtlasDOPower, AtlasDOi2c_addr);
#else
// AtlasScientificDO atlasDO(AtlasDOPower, AtlasDOi2c_addr);
AtlasScientificDO atlasDO(AtlasDOPower);
#endif

// Create concentration and percent saturation variable pointers for the EZO-DO
Variable* atlasDOconc = new AtlasScientificDO_DOmgL(
    &atlasDO, "12345678-abcd-1234-ef00-1234567890ab");
Variable* atlasDOpct = new AtlasScientificDO_DOpct(
    &atlasDO, "12345678-abcd-1234-ef00-1234567890ab");
/** End [atlas_do] */
#endif

#if defined MS_BUILD_TEST_ATLASPH || defined MS_BUILD_TEST_ALL_SENSORS
// ==========================================================================
//  Atlas Scientific EZO-pH Sensor
// ==========================================================================
/** Start [atlas_ph] */
#include <sensors/AtlasScientificpH.h>

const int8_t AtlaspHPower    = sensorPowerPin;  // Power pin (-1 if unconnected)
uint8_t      AtlaspHi2c_addr = 0x63;            // Default for pH is 0x63 (99)
// All Atlas sensors have different default I2C addresses, but any of them can
// be re-addressed to any 8 bit number.  If using the default address for any
// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific pH sensor object
#ifdef MS_ATLAS_SOFTWAREWIRE
AtlasScientificpH atlaspH(&softI2C, AtlaspHPower, AtlaspHi2c_addr);
// AtlasScientificpH atlaspH(AtlaspHPower, softwareSDA, softwareSCL,
//                           AtlaspHi2c_addr);
#else
// AtlasScientificpH atlaspH(AtlaspHPower, AtlaspHi2c_addr);
AtlasScientificpH atlaspH(AtlaspHPower);
#endif

// Create a pH variable pointer for the pH sensor
Variable* atlaspHpH =
    new AtlasScientificpH_pH(&atlaspH, "12345678-abcd-1234-ef00-1234567890ab");
/** End [atlas_ph] */
#endif


#if defined MS_BUILD_TEST_ATLASRTD || defined MS_BUILD_TEST_ATLASEC || \
    defined                                   MS_BUILD_TEST_ALL_SENSORS
// ==========================================================================
//  Atlas Scientific EZO-RTD Temperature Sensor
// ==========================================================================
/** Start [atlas_rtd] */
#include <sensors/AtlasScientificRTD.h>

const int8_t AtlasRTDPower = sensorPowerPin;  // Power pin (-1 if unconnected)
uint8_t      AtlasRTDi2c_addr = 0x66;         // Default for RTD is 0x66 (102)
// All Atlas sensors have different default I2C addresses, but any of them can
// be re-addressed to any 8 bit number.  If using the default address for any
// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific RTD sensor object
#ifdef MS_ATLAS_SOFTWAREWIRE
AtlasScientificRTD atlasRTD(&softI2C, AtlasRTDPower, AtlasRTDi2c_addr);
// AtlasScientificRTD atlasRTD(AtlasRTDPower, softwareSDA, softwareSCL,
//                             AtlasRTDi2c_addr);
#else
// AtlasScientificRTD atlasRTD(AtlasRTDPower, AtlasRTDi2c_addr);
AtlasScientificRTD atlasRTD(AtlasRTDPower);
#endif

// Create a temperature variable pointer for the RTD
Variable* atlasTemp = new AtlasScientificRTD_Temp(
    &atlasRTD, "12345678-abcd-1234-ef00-1234567890ab");
/** End [atlas_rtd] */
#endif


#if defined MS_BUILD_TEST_ATLASEC || defined MS_BUILD_TEST_ALL_SENSORS
// ==========================================================================
//  Atlas Scientific EZO-EC Conductivity Sensor
// ==========================================================================
/** Start [atlas_ec] */
#include <sensors/AtlasScientificEC.h>

const int8_t AtlasECPower    = sensorPowerPin;  // Power pin (-1 if unconnected)
uint8_t      AtlasECi2c_addr = 0x64;            // Default for EC is 0x64 (100)
// All Atlas sensors have different default I2C addresses, but any of them can
// be re-addressed to any 8 bit number.  If using the default address for any
// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific Conductivity sensor object
#ifdef MS_ATLAS_SOFTWAREWIRE
// AtlasScientificEC atlasEC(AtlasECPower, softwareSDA, softwareSCL,
//                           AtlasECi2c_addr);
AtlasScientificEC atlasEC(&softI2C, AtlasECPower, AtlasECi2c_addr);
#else
// AtlasScientificEC atlasEC(AtlasECPower, AtlasECi2c_addr);
AtlasScientificEC atlasEC(AtlasECPower);
#endif

// Create four variable pointers for the EZO-ES
Variable* atlasCond = new AtlasScientificEC_Cond(
    &atlasEC, "12345678-abcd-1234-ef00-1234567890ab");
Variable* atlasTDS =
    new AtlasScientificEC_TDS(&atlasEC, "12345678-abcd-1234-ef00-1234567890ab");
Variable* atlasSal = new AtlasScientificEC_Salinity(
    &atlasEC, "12345678-abcd-1234-ef00-1234567890ab");
Variable* atlasGrav = new AtlasScientificEC_SpecificGravity(
    &atlasEC, "12345678-abcd-1234-ef00-1234567890ab");

// Create a calculated variable for the temperature compensated conductivity
// (that is, the specific conductance).  For this example, we will use the
// temperature measured by the Atlas RTD above this.  You could use the
// temperature returned by any other water temperature sensor if desired.
// **DO NOT** use your logger board temperature (ie, from the DS3231) to
// calculate specific conductance!
float calculateAtlasSpCond(void) {
    float spCond    = -9999;  // Always safest to start with a bad value
    float waterTemp = atlasTemp->getValue();
    float rawCond   = atlasCond->getValue();
    // ^^ Linearized temperature correction coefficient per degrees Celsius.
    // The value of 0.019 comes from measurements reported here:
    // Hayashi M. Temperature-electrical conductivity relation of water for
    // environmental monitoring and geophysical data inversion. Environ Monit
    // Assess. 2004 Aug-Sep;96(1-3):119-28.
    // doi: 10.1023/b:emas.0000031719.83065.68. PMID: 15327152.
    if (waterTemp != -9999 && rawCond != -9999) {
        // make sure both inputs are good
        float temperatureCoef = 0.019;
        spCond = rawCond / (1 + temperatureCoef * (waterTemp - 25.0));
    }
    return spCond;
}

// Properties of the calculated variable
// The number of digits after the decimal place
const uint8_t atlasSpCondResolution = 0;
// This must be a value from http://vocabulary.odm2.org/variablename/
const char* atlasSpCondName = "specificConductance";
// This must be a value from http://vocabulary.odm2.org/units/
const char* atlasSpCondUnit = "microsiemenPerCentimeter";
// A short code for the variable
const char* atlasSpCondCode = "atlasSpCond";
// The (optional) universallly unique identifier
const char* atlasSpCondUUID = "12345678-abcd-1234-ef00-1234567890ab";

// Finally, create the specific conductance variable and return a pointer to it
Variable* atlasSpCond =
    new Variable(calculateAtlasSpCond, atlasSpCondResolution, atlasSpCondName,
                 atlasSpCondUnit, atlasSpCondCode, atlasSpCondUUID);
/** End [atlas_ec] */
#endif

// ==========================================================================
//  Creating the Variable Array[s] and Filling with Variable Objects
// ==========================================================================
/** Start [variable_arrays] */
Variable* variableList[] = {
//    new DecagonCTD_Cond(&ctd),
//    new DecagonCTD_Temp(&ctd),
//    new DecagonCTD_Depth(&ctd),
//    new CampbellOBS3_Turbidity(&osb3low, "", "TurbLow"),
//    new CampbellOBS3_Turbidity(&osb3high, "", "TurbHigh"),
    new ProcessorStats_Battery(&mcuBoard),
    new MaximDS3231_Temp(&ds3231),
//    new Modem_RSSI(&modem),
    new Modem_SignalPercent(&modem),
};

// All UUID's, device registration, and sampling feature information can be
// pasted directly from Monitor My Watershed.  To get the list, click the "View
// token UUID list" button on the upper right of the site page.

// *** CAUTION --- CAUTION --- CAUTION --- CAUTION --- CAUTION ***
// Check the order of your variables in the variable list!!!
// Be VERY certain that they match the order of your UUID's!
// Rearrange the variables in the variable list if necessary to match!
// *** CAUTION --- CAUTION --- CAUTION --- CAUTION --- CAUTION ***
const char* UUIDs[] = {
    "12345678-abcd-1234-ef00-1234567890ab",  // Electrical conductivity
                                             // (Decagon_CTD-10_Cond)
    "12345678-abcd-1234-ef00-1234567890ab",  // Temperature
                                             // (Decagon_CTD-10_Temp)
    "12345678-abcd-1234-ef00-1234567890ab",  // Water depth
                                             // (Decagon_CTD-10_Depth)
    "12345678-abcd-1234-ef00-1234567890ab",  // Turbidity (Campbell_OBS3_Turb)
    "12345678-abcd-1234-ef00-1234567890ab",  // Turbidity (Campbell_OBS3_Turb)
    "12345678-abcd-1234-ef00-1234567890ab",  // Battery voltage
                                             // (EnviroDIY_Mayfly_Batt)
    "12345678-abcd-1234-ef00-1234567890ab",  // Temperature
                                             // (EnviroDIY_Mayfly_Temp)
    "12345678-abcd-1234-ef00-1234567890ab",  // Received signal strength
                                             // indication (Digi_Cellular_RSSI)
    "12345678-abcd-1234-ef00-1234567890ab"   // Percent full scale
                                             // (Digi_Cellular_SignalPercent)
};
const char* registrationToken =
    "12345678-abcd-1234-ef00-1234567890ab";  // Device registration token
const char* samplingFeature =
    "12345678-abcd-1234-ef00-1234567890ab";  // Sampling feature UUID

// Count up the number of pointers in the array
int variableCount = sizeof(variableList) / sizeof(variableList[0]);

// Create the VariableArray object
VariableArray varArray(variableCount, variableList, UUIDs);
/** End [variable_arrays] */


// ==========================================================================
//  The Logger Object[s]
// ==========================================================================
/** Start [loggers] */
// Create a new logger instance
Logger dataLogger(LoggerID, loggingInterval, &varArray);
/** End [loggers] */


// ==========================================================================
//  Creating Data Publisher[s]
// ==========================================================================
/** Start [publishers] */
// Create a data publisher for the Monitor My Watershed/EnviroDIY POST endpoint
#include <publishers/EnviroDIYPublisher.h>
EnviroDIYPublisher EnviroDIYPOST(dataLogger, &modem.gsmClient,
                                 registrationToken, samplingFeature);
/** End [publishers] */


// ==========================================================================
//  Working Functions
// ==========================================================================
/** Start [working_functions] */
// Flashes the LED's on the primary board
void greenredflash(uint8_t numFlash = 4, uint8_t rate = 75) {
    for (uint8_t i = 0; i < numFlash; i++) {
        digitalWrite(greenLED, HIGH);
        digitalWrite(redLED, LOW);
        delay(rate);
        digitalWrite(greenLED, LOW);
        digitalWrite(redLED, HIGH);
        delay(rate);
    }
    digitalWrite(redLED, LOW);
}

// Reads the battery voltage
// NOTE: This will actually return the battery level from the previous update!
float getBatteryVoltage() {
    if (mcuBoard.sensorValues[0] == -9999) mcuBoard.update();
    return mcuBoard.sensorValues[0];
}


// ==========================================================================
// Arduino Setup Function
// ==========================================================================
/** Start [setup] */
void setup() {
    // Start the primary serial connection
    Serial.begin(serialBaud);

    // Print a start-up note to the first serial port
    Serial.print(F("Now running "));
    Serial.print(sketchName);
    Serial.print(F(" on Logger "));
    Serial.println(LoggerID);
    Serial.println();

    Serial.print(F("Using ModularSensors Library version "));
    Serial.println(MODULAR_SENSORS_VERSION);
    Serial.print(F("TinyGSM Library version "));
    Serial.println(TINYGSM_VERSION);
    Serial.println();

    // Start the serial connection with the modem
    modemSerial.begin(modemBaud);

    // Set up pins for the LED's
    pinMode(greenLED, OUTPUT);
    digitalWrite(greenLED, LOW);
    pinMode(redLED, OUTPUT);
    digitalWrite(redLED, LOW);
    // Blink the LEDs to show the board is on and starting up
    greenredflash();

    // Set the timezones for the logger/data and the RTC
    // Logging in the given time zone
    Logger::setLoggerTimeZone(timeZone);
    // It is STRONGLY RECOMMENDED that you set the RTC to be in UTC (UTC+0)
    Logger::setRTCTimeZone(0);

    // Attach the modem and information pins to the logger
    dataLogger.attachModem(modem);
    modem.setModemLED(modemLEDPin);
    dataLogger.setLoggerPins(wakePin, sdCardSSPin, sdCardPwrPin, buttonPin,
                             greenLED);

    // Begin the logger
    dataLogger.begin();

    // Note:  Please change these battery voltages to match your battery
    // Set up the sensors, except at lowest battery level
    if (getBatteryVoltage() > 3.4) {
        Serial.println(F("Setting up sensors..."));
        varArray.setupSensors();
    }

    // Extra modem set-up - selecting AT&T as the carrier and LTE-M only
    // NOTE:  The code for this could be shortened using the "commandMode" and
    // other XBee specific commands in TinyGSM.  I've written it this way in
    // this example to show how the settings could be changed in either bypass
    // OR transparent mode.
    Serial.println(F("Waking modem and setting Cellular Carrier Options..."));
    modem.modemWake();  // NOTE:  This will also set up the modem
    // Go back to command mode to set carrier options
    for (uint8_t i = 0; i < 5; i++) {
        // Wait the required guard time before entering command mode
        delay(1010);
        modem.gsmModem.streamWrite(GF("+++"));  // enter command mode
        if (modem.gsmModem.waitResponse(2000, GF("OK\r")) == 1) break;
    }
    // Carrier Profile - 0 = Automatic selection
    //                 - 1 = No profile/SIM ICCID selected
    //                 - 2 = AT&T
    //                 - 3 = Verizon
    // NOTE:  To select T-Mobile, you must enter bypass mode!
    modem.gsmModem.sendAT(GF("CP"), 2);
    modem.gsmModem.waitResponse(GF("OK\r"));
    // Cellular network technology - 0 = LTE-M with NB-IoT fallback
    //                             - 1 = NB-IoT with LTE-M fallback
    //                             - 2 = LTE-M only
    //                             - 3 = NB-IoT only
    modem.gsmModem.sendAT(GF("N#"), 2);
    modem.gsmModem.waitResponse();
    // Write changes to flash and apply them
    Serial.println(F("Wait while applying changes..."));
    // Write changes to flash
    modem.gsmModem.sendAT(GF("WR"));
    modem.gsmModem.waitResponse(GF("OK\r"));
    // Apply changes
    modem.gsmModem.sendAT(GF("AC"));
    modem.gsmModem.waitResponse(GF("OK\r"));
    // Reset the cellular component to ensure network settings are changed
    modem.gsmModem.sendAT(GF("!R"));
    modem.gsmModem.waitResponse(30000L, GF("OK\r"));
    // Force reset of the Digi component as well
    // This effectively exits command mode
    modem.gsmModem.sendAT(GF("FR"));
    modem.gsmModem.waitResponse(5000L, GF("OK\r"));

    // Sync the clock if it isn't valid or we have battery to spare
    if (getBatteryVoltage() > 3.55 || !dataLogger.isRTCSane()) {
        // Synchronize the RTC with NIST
        // This will also set up the modem
        dataLogger.syncRTC();
    }

    // Create the log file, adding the default header to it
    // Do this last so we have the best chance of getting the time correct and
    // all sensor names correct
    // Writing to the SD card can be power intensive, so if we're skipping
    // the sensor setup we'll skip this too.
    if (getBatteryVoltage() > 3.4) {
        Serial.println(F("Setting up file on SD card"));
        dataLogger.turnOnSDcard(
            true);  // true = wait for card to settle after power up
        dataLogger.createLogFile(true);  // true = write a new header
        dataLogger.turnOffSDcard(
            true);  // true = wait for internal housekeeping after write
    }

    // Call the processor sleep
    Serial.println(F("Putting processor to sleep\n"));
    dataLogger.systemSleep();
}
/** End [setup] */


// ==========================================================================
//  Arduino Loop Function
// ==========================================================================
/** Start [loop] */
// Use this short loop for simple data logging and sending
void loop() {
    // Note:  Please change these battery voltages to match your battery
    // At very low battery, just go back to sleep
    if (getBatteryVoltage() < 3.4) {
        dataLogger.systemSleep();
    }
    // At moderate voltage, log data but don't send it over the modem
    else if (getBatteryVoltage() < 3.55) {
        dataLogger.logData();
    }
    // If the battery is good, send the data to the world
    else {
        dataLogger.logDataAndPublish();
    }
}
/** End [loop] */

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/** =========================================================================

* @file DRWI_LTE.ino

* @brief Example for DRWI CitSci LTE sites.

* @author Sara Geleskie Damiano <sdamiano@stroudcenter.org>

* and the EnviroDIY Development Team

* This example is published under the BSD-3 license.

* Build Environment: Visual Studios Code with PlatformIO

* Hardware Platform: EnviroDIY Mayfly Arduino Datalogger

* DISCLAIMER:

* THIS CODE IS PROVIDED "AS IS" - NO WARRANTY IS GIVEN.

* ======================================================================= */

// ==========================================================================

// Defines for the Arduino IDE

// NOTE: These are ONLY needed to compile with the Arduino IDE.

// If you use PlatformIO, you should set these build flags in your

// platformio.ini

// ==========================================================================

/** Start [defines] */

#ifndef TINY_GSM_RX_BUFFER

#define TINY_GSM_RX_BUFFER 64

#endif

#ifndef TINY_GSM_YIELD_MS

#define TINY_GSM_YIELD_MS 2

#endif

/** End [defines] */

// ==========================================================================

// Include the libraries required for any data logger

// ==========================================================================

/** Start [includes] */

// The Arduino library is needed for every Arduino program.

#include <Arduino.h>

// EnableInterrupt is used by ModularSensors for external and pin change

// interrupts and must be explicitly included in the main program.

#include <EnableInterrupt.h>

// To get all of the base classes for ModularSensors, include LoggerBase.

// NOTE: Individual sensor definitions must be included separately.

#include <LoggerBase.h>

/** End [includes] */

// ==========================================================================

// Data Logging Options

// ==========================================================================

/** Start [logging_options] */

// The name of this program file

const char* sketchName = "DRWI_LTE.ino";

// Logger ID, also becomes the prefix for the name of the data file on SD card

const char* LoggerID = "XXXXX";

// How frequently (in minutes) to log data

const uint8_t loggingInterval = 5;

// Your logger's timezone.

const int8_t timeZone = -5; // Eastern Standard Time

// NOTE: Daylight savings time will not be applied! Please use standard time!

// Set the input and output pins for the logger

// NOTE: Use -1 for pins that do not apply

const int32_t serialBaud = 115200; // Baud rate for debugging

const int8_t greenLED = 8; // Pin for the green LED

const int8_t redLED = 9; // Pin for the red LED

const int8_t buttonPin = 21; // Pin for debugging mode (ie, button pin)

const int8_t wakePin = A7; // MCU interrupt/alarm pin to wake from sleep

// Set the wake pin to -1 if you do not want the main processor to sleep.

// In a SAMD system where you are using the built-in rtc, set wakePin to 1

const int8_t sdCardPwrPin = -1; // MCU SD card power pin

const int8_t sdCardSSPin = 12; // SD card chip select/slave select pin

const int8_t sensorPowerPin = 22; // MCU pin controlling main sensor power

/** End [logging_options] */

// ==========================================================================

// Wifi/Cellular Modem Options

// ==========================================================================

/** Start [xbee_cell_transparent] */

// For any Digi Cellular XBee's

// NOTE: The u-blox based Digi XBee's (3G global and LTE-M global)

// are more stable used in bypass mode (below)

// The Telit based Digi XBees (LTE Cat1) can only use this mode.

#include <modems/DigiXBeeCellularTransparent.h>

// Create a reference to the serial port for the modem

HardwareSerial& modemSerial = Serial1; // Use hardware serial if possible

const int32_t modemBaud = 9600; // All XBee's use 9600 by default

// Modem Pins - Describe the physical pin connection of your modem to your board

// NOTE: Use -1 for pins that do not apply

const int8_t modemVccPin = -2; // MCU pin controlling modem power

const int8_t modemStatusPin = 19; // MCU pin used to read modem status

const bool useCTSforStatus = false; // Flag to use the modem CTS pin for status

const int8_t modemResetPin = 20; // MCU pin connected to modem reset pin

const int8_t modemSleepRqPin = 23; // MCU pin for modem sleep/wake request

const int8_t modemLEDPin = redLED; // MCU pin connected an LED to show modem

// status (-1 if unconnected)

// Network connection information

const char* apn = "hologram"; // The APN for the gprs connection

DigiXBeeCellularTransparent modemXBCT(&modemSerial, modemVccPin, modemStatusPin,

useCTSforStatus, modemResetPin,

modemSleepRqPin, apn);

// Create an extra reference to the modem by a generic name

DigiXBeeCellularTransparent modem = modemXBCT;

/** End [xbee_cell_transparent] */

// ==========================================================================

// Using the Processor as a Sensor

// ==========================================================================

/** Start [processor_sensor] */

#include <sensors/ProcessorStats.h>

// Create the main processor chip "sensor" - for general metadata

const char* mcuBoardVersion = "v0.5b";

ProcessorStats mcuBoard(mcuBoardVersion);

/** End [processor_sensor] */

// ==========================================================================

// Maxim DS3231 RTC (Real Time Clock)

// ==========================================================================

/** Start [ds3231] */

#include <sensors/MaximDS3231.h>

// Create a DS3231 sensor object

MaximDS3231 ds3231(1);

/** End [ds3231] */

#if defined MS_BUILD_TEST_ATLASDO || defined MS_BUILD_TEST_ALL_SENSORS

// ==========================================================================

// Atlas Scientific EZO-DO Dissolved Oxygen Sensor

// ==========================================================================

/** Start [atlas_do] */

#include <sensors/AtlasScientificDO.h>

const int8_t AtlasDOPower = sensorPowerPin; // Power pin (-1 if unconnected)

uint8_t AtlasDOi2c_addr = 0x61; // Default for DO is 0x61 (97)

// All Atlas sensors have different default I2C addresses, but any of them can

// be re-addressed to any 8 bit number. If using the default address for any

// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific DO sensor object

#ifdef MS_ATLAS_SOFTWAREWIRE

// AtlasScientificDO atlasDO(AtlasDOPower, softwareSDA, softwareSCL,

// AtlasDOi2c_addr);

AtlasScientificDO atlasDO(&softI2C, AtlasDOPower, AtlasDOi2c_addr);

#else

// AtlasScientificDO atlasDO(AtlasDOPower, AtlasDOi2c_addr);

AtlasScientificDO atlasDO(AtlasDOPower);

#endif

// Create concentration and percent saturation variable pointers for the EZO-DO

Variable* atlasDOconc = new AtlasScientificDO_DOmgL(

&atlasDO, "12345678-abcd-1234-ef00-1234567890ab");

Variable* atlasDOpct = new AtlasScientificDO_DOpct(

&atlasDO, "12345678-abcd-1234-ef00-1234567890ab");

/** End [atlas_do] */

#endif

#if defined MS_BUILD_TEST_ATLASPH || defined MS_BUILD_TEST_ALL_SENSORS

// ==========================================================================

// Atlas Scientific EZO-pH Sensor

// ==========================================================================

/** Start [atlas_ph] */

#include <sensors/AtlasScientificpH.h>

const int8_t AtlaspHPower = sensorPowerPin; // Power pin (-1 if unconnected)

uint8_t AtlaspHi2c_addr = 0x63; // Default for pH is 0x63 (99)

// All Atlas sensors have different default I2C addresses, but any of them can

// be re-addressed to any 8 bit number. If using the default address for any

// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific pH sensor object

#ifdef MS_ATLAS_SOFTWAREWIRE

AtlasScientificpH atlaspH(&softI2C, AtlaspHPower, AtlaspHi2c_addr);

// AtlasScientificpH atlaspH(AtlaspHPower, softwareSDA, softwareSCL,

// AtlaspHi2c_addr);

#else

// AtlasScientificpH atlaspH(AtlaspHPower, AtlaspHi2c_addr);

AtlasScientificpH atlaspH(AtlaspHPower);

#endif

// Create a pH variable pointer for the pH sensor

Variable* atlaspHpH =

new AtlasScientificpH_pH(&atlaspH, "12345678-abcd-1234-ef00-1234567890ab");

/** End [atlas_ph] */

#endif

#if defined MS_BUILD_TEST_ATLASRTD || defined MS_BUILD_TEST_ATLASEC || \

defined MS_BUILD_TEST_ALL_SENSORS

// ==========================================================================

// Atlas Scientific EZO-RTD Temperature Sensor

// ==========================================================================

/** Start [atlas_rtd] */

#include <sensors/AtlasScientificRTD.h>

const int8_t AtlasRTDPower = sensorPowerPin; // Power pin (-1 if unconnected)

uint8_t AtlasRTDi2c_addr = 0x66; // Default for RTD is 0x66 (102)

// All Atlas sensors have different default I2C addresses, but any of them can

// be re-addressed to any 8 bit number. If using the default address for any

// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific RTD sensor object

#ifdef MS_ATLAS_SOFTWAREWIRE

AtlasScientificRTD atlasRTD(&softI2C, AtlasRTDPower, AtlasRTDi2c_addr);

// AtlasScientificRTD atlasRTD(AtlasRTDPower, softwareSDA, softwareSCL,

// AtlasRTDi2c_addr);

#else

// AtlasScientificRTD atlasRTD(AtlasRTDPower, AtlasRTDi2c_addr);

AtlasScientificRTD atlasRTD(AtlasRTDPower);

#endif

// Create a temperature variable pointer for the RTD

Variable* atlasTemp = new AtlasScientificRTD_Temp(

&atlasRTD, "12345678-abcd-1234-ef00-1234567890ab");

/** End [atlas_rtd] */

#endif

#if defined MS_BUILD_TEST_ATLASEC || defined MS_BUILD_TEST_ALL_SENSORS

// ==========================================================================

// Atlas Scientific EZO-EC Conductivity Sensor

// ==========================================================================

/** Start [atlas_ec] */

#include <sensors/AtlasScientificEC.h>

const int8_t AtlasECPower = sensorPowerPin; // Power pin (-1 if unconnected)

uint8_t AtlasECi2c_addr = 0x64; // Default for EC is 0x64 (100)

// All Atlas sensors have different default I2C addresses, but any of them can

// be re-addressed to any 8 bit number. If using the default address for any

// Atlas Scientific sensor, you may omit this argument.

// Create an Atlas Scientific Conductivity sensor object

#ifdef MS_ATLAS_SOFTWAREWIRE

// AtlasScientificEC atlasEC(AtlasECPower, softwareSDA, softwareSCL,

// AtlasECi2c_addr);

AtlasScientificEC atlasEC(&softI2C, AtlasECPower, AtlasECi2c_addr);

#else

// AtlasScientificEC atlasEC(AtlasECPower, AtlasECi2c_addr);

AtlasScientificEC atlasEC(AtlasECPower);

#endif

// Create four variable pointers for the EZO-ES

Variable* atlasCond = new AtlasScientificEC_Cond(

&atlasEC, "12345678-abcd-1234-ef00-1234567890ab");

Variable* atlasTDS =

new AtlasScientificEC_TDS(&atlasEC, "12345678-abcd-1234-ef00-1234567890ab");

Variable* atlasSal = new AtlasScientificEC_Salinity(

&atlasEC, "12345678-abcd-1234-ef00-1234567890ab");

Variable* atlasGrav = new AtlasScientificEC_SpecificGravity(

&atlasEC, "12345678-abcd-1234-ef00-1234567890ab");

// Create a calculated variable for the temperature compensated conductivity

// (that is, the specific conductance). For this example, we will use the

// temperature measured by the Atlas RTD above this. You could use the

// temperature returned by any other water temperature sensor if desired.

// **DO NOT** use your logger board temperature (ie, from the DS3231) to

// calculate specific conductance!

float calculateAtlasSpCond(void) {

float spCond = -9999; // Always safest to start with a bad value

float waterTemp = atlasTemp->getValue();

float rawCond = atlasCond->getValue();

// ^^ Linearized temperature correction coefficient per degrees Celsius.

// The value of 0.019 comes from measurements reported here:

// Hayashi M. Temperature-electrical conductivity relation of water for

// environmental monitoring and geophysical data inversion. Environ Monit

// Assess. 2004 Aug-Sep;96(1-3):119-28.

// doi: 10.1023/b:emas.0000031719.83065.68. PMID: 15327152.

if (waterTemp != -9999 && rawCond != -9999) {

// make sure both inputs are good

float temperatureCoef = 0.019;

spCond = rawCond / (1 + temperatureCoef * (waterTemp - 25.0));

}

return spCond;

}

// Properties of the calculated variable

// The number of digits after the decimal place

const uint8_t atlasSpCondResolution = 0;

// This must be a value from http://vocabulary.odm2.org/variablename/

const char* atlasSpCondName = "specificConductance";

// This must be a value from http://vocabulary.odm2.org/units/

const char* atlasSpCondUnit = "microsiemenPerCentimeter";

// A short code for the variable

const char* atlasSpCondCode = "atlasSpCond";

// The (optional) universallly unique identifier

const char* atlasSpCondUUID = "12345678-abcd-1234-ef00-1234567890ab";

// Finally, create the specific conductance variable and return a pointer to it

Variable* atlasSpCond =

new Variable(calculateAtlasSpCond, atlasSpCondResolution, atlasSpCondName,

atlasSpCondUnit, atlasSpCondCode, atlasSpCondUUID);

/** End [atlas_ec] */

#endif

// ==========================================================================

// Creating the Variable Array[s] and Filling with Variable Objects

// ==========================================================================

/** Start [variable_arrays] */

Variable* variableList[] = {

// new DecagonCTD_Cond(&ctd),

// new DecagonCTD_Temp(&ctd),

// new DecagonCTD_Depth(&ctd),

// new CampbellOBS3_Turbidity(&osb3low, "", "TurbLow"),

// new CampbellOBS3_Turbidity(&osb3high, "", "TurbHigh"),

new ProcessorStats_Battery(&mcuBoard),

new MaximDS3231_Temp(&ds3231),

// new Modem_RSSI(&modem),

new Modem_SignalPercent(&modem),

};

// All UUID's, device registration, and sampling feature information can be

// pasted directly from Monitor My Watershed. To get the list, click the "View

// token UUID list" button on the upper right of the site page.

// *** CAUTION --- CAUTION --- CAUTION --- CAUTION --- CAUTION ***

// Check the order of your variables in the variable list!!!

// Be VERY certain that they match the order of your UUID's!

// Rearrange the variables in the variable list if necessary to match!

// *** CAUTION --- CAUTION --- CAUTION --- CAUTION --- CAUTION ***

const char* UUIDs[] = {

"12345678-abcd-1234-ef00-1234567890ab", // Electrical conductivity

// (Decagon_CTD-10_Cond)

"12345678-abcd-1234-ef00-1234567890ab", // Temperature

// (Decagon_CTD-10_Temp)

"12345678-abcd-1234-ef00-1234567890ab", // Water depth

// (Decagon_CTD-10_Depth)

"12345678-abcd-1234-ef00-1234567890ab", // Turbidity (Campbell_OBS3_Turb)

"12345678-abcd-1234-ef00-1234567890ab", // Battery voltage

// (EnviroDIY_Mayfly_Batt)

"12345678-abcd-1234-ef00-1234567890ab", // Temperature

// (EnviroDIY_Mayfly_Temp)

"12345678-abcd-1234-ef00-1234567890ab", // Received signal strength

// indication (Digi_Cellular_RSSI)

"12345678-abcd-1234-ef00-1234567890ab" // Percent full scale

// (Digi_Cellular_SignalPercent)

};

const char* registrationToken =

"12345678-abcd-1234-ef00-1234567890ab"; // Device registration token

const char* samplingFeature =

"12345678-abcd-1234-ef00-1234567890ab"; // Sampling feature UUID

// Count up the number of pointers in the array

int variableCount = sizeof(variableList) / sizeof(variableList[0]);

// Create the VariableArray object

VariableArray varArray(variableCount, variableList, UUIDs);

/** End [variable_arrays] */

// ==========================================================================

// The Logger Object[s]

// ==========================================================================

/** Start [loggers] */

// Create a new logger instance

Logger dataLogger(LoggerID, loggingInterval, &varArray);

/** End [loggers] */

// ==========================================================================

// Creating Data Publisher[s]

// ==========================================================================

/** Start [publishers] */

// Create a data publisher for the Monitor My Watershed/EnviroDIY POST endpoint

#include <publishers/EnviroDIYPublisher.h>

EnviroDIYPublisher EnviroDIYPOST(dataLogger, &modem.gsmClient,

registrationToken, samplingFeature);

/** End [publishers] */

// ==========================================================================

// Working Functions

// ==========================================================================

/** Start [working_functions] */

// Flashes the LED's on the primary board

void greenredflash(uint8_t numFlash = 4, uint8_t rate = 75) {

for (uint8_t i = 0; i < numFlash; i++) {

digitalWrite(greenLED, HIGH);

digitalWrite(redLED, LOW);

delay(rate);

digitalWrite(greenLED, LOW);

digitalWrite(redLED, HIGH);

delay(rate);

}

digitalWrite(redLED, LOW);

}

// Reads the battery voltage

// NOTE: This will actually return the battery level from the previous update!

float getBatteryVoltage() {

if (mcuBoard.sensorValues[0] == -9999) mcuBoard.update();

return mcuBoard.sensorValues[0];

}

// ==========================================================================

// Arduino Setup Function

// ==========================================================================

/** Start [setup] */

void setup() {

// Start the primary serial connection

Serial.begin(serialBaud);

// Print a start-up note to the first serial port

Serial.print(F("Now running "));

Serial.print(sketchName);

Serial.print(F(" on Logger "));

Serial.println(LoggerID);

Serial.println();

Serial.print(F("Using ModularSensors Library version "));

Serial.println(MODULAR_SENSORS_VERSION);

Serial.print(F("TinyGSM Library version "));

Serial.println(TINYGSM_VERSION);

Serial.println();

// Start the serial connection with the modem

modemSerial.begin(modemBaud);

// Set up pins for the LED's

pinMode(greenLED, OUTPUT);

digitalWrite(greenLED, LOW);

pinMode(redLED, OUTPUT);

digitalWrite(redLED, LOW);

// Blink the LEDs to show the board is on and starting up

greenredflash();

// Set the timezones for the logger/data and the RTC

// Logging in the given time zone

Logger::setLoggerTimeZone(timeZone);

// It is STRONGLY RECOMMENDED that you set the RTC to be in UTC (UTC+0)

Logger::setRTCTimeZone(0);

// Attach the modem and information pins to the logger

dataLogger.attachModem(modem);

modem.setModemLED(modemLEDPin);

dataLogger.setLoggerPins(wakePin, sdCardSSPin, sdCardPwrPin, buttonPin,

greenLED);

// Begin the logger

dataLogger.begin();

// Note: Please change these battery voltages to match your battery

// Set up the sensors, except at lowest battery level

if (getBatteryVoltage() > 3.4) {

Serial.println(F("Setting up sensors..."));

varArray.setupSensors();

}

// Extra modem set-up - selecting AT&T as the carrier and LTE-M only

// NOTE: The code for this could be shortened using the "commandMode" and

// other XBee specific commands in TinyGSM. I've written it this way in

// this example to show how the settings could be changed in either bypass

// OR transparent mode.

Serial.println(F("Waking modem and setting Cellular Carrier Options..."));

modem.modemWake(); // NOTE: This will also set up the modem

// Go back to command mode to set carrier options

for (uint8_t i = 0; i < 5; i++) {

// Wait the required guard time before entering command mode

delay(1010);

modem.gsmModem.streamWrite(GF("+++")); // enter command mode

if (modem.gsmModem.waitResponse(2000, GF("OK\r")) == 1) break;

}

// Carrier Profile - 0 = Automatic selection

// - 1 = No profile/SIM ICCID selected

// - 2 = AT&T

// - 3 = Verizon

// NOTE: To select T-Mobile, you must enter bypass mode!

modem.gsmModem.sendAT(GF("CP"), 2);

modem.gsmModem.waitResponse(GF("OK\r"));

// Cellular network technology - 0 = LTE-M with NB-IoT fallback

// - 1 = NB-IoT with LTE-M fallback

// - 2 = LTE-M only

// - 3 = NB-IoT only

modem.gsmModem.sendAT(GF("N#"), 2);

modem.gsmModem.waitResponse();

// Write changes to flash and apply them

Serial.println(F("Wait while applying changes..."));

// Write changes to flash

modem.gsmModem.sendAT(GF("WR"));

modem.gsmModem.waitResponse(GF("OK\r"));

// Apply changes

modem.gsmModem.sendAT(GF("AC"));

modem.gsmModem.waitResponse(GF("OK\r"));

// Reset the cellular component to ensure network settings are changed

modem.gsmModem.sendAT(GF("!R"));

modem.gsmModem.waitResponse(30000L, GF("OK\r"));

// Force reset of the Digi component as well

// This effectively exits command mode

modem.gsmModem.sendAT(GF("FR"));

modem.gsmModem.waitResponse(5000L, GF("OK\r"));

// Sync the clock if it isn't valid or we have battery to spare

if (getBatteryVoltage() > 3.55 || !dataLogger.isRTCSane()) {

// Synchronize the RTC with NIST

// This will also set up the modem

dataLogger.syncRTC();

}

// Create the log file, adding the default header to it

// Do this last so we have the best chance of getting the time correct and

// all sensor names correct

// Writing to the SD card can be power intensive, so if we're skipping

// the sensor setup we'll skip this too.

if (getBatteryVoltage() > 3.4) {

Serial.println(F("Setting up file on SD card"));

dataLogger.turnOnSDcard(

true); // true = wait for card to settle after power up

dataLogger.createLogFile(true); // true = write a new header

dataLogger.turnOffSDcard(

true); // true = wait for internal housekeeping after write

}

// Call the processor sleep

Serial.println(F("Putting processor to sleep\n"));

dataLogger.systemSleep();

}

/** End [setup] */

// ==========================================================================

// Arduino Loop Function

// ==========================================================================

/** Start [loop] */

// Use this short loop for simple data logging and sending

void loop() {

// Note: Please change these battery voltages to match your battery

// At very low battery, just go back to sleep

if (getBatteryVoltage() < 3.4) {

dataLogger.systemSleep();

}

// At moderate voltage, log data but don't send it over the modem

else if (getBatteryVoltage() < 3.55) {

dataLogger.logData();

}

// If the battery is good, send the data to the world

else {

dataLogger.logDataAndPublish();

}

/** End [loop] */

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