Merge pull request adafruit#1079 from jedgarpark/pulse-ox-log

includes RTC date/time and data logging to SD card.

Author: jedgarpark

Pulse_Oximeter_Logger/pulse_oximeter_logger.py

@@ -0,0 +1,143 @@
+"""
+Read data from a BerryMed pulse oximeter, model BM1000C, BM1000E, etc.
+Run this on Feather nRF52840
+Log data to SD card on Autologger FeatherWing
+"""
+
+# Protocol defined here:
+#     https://github.com/zh2x/BCI_Protocol
+# Thanks as well to:
+#     https://github.com/ehborisov/BerryMed-Pulse-Oximeter-tool
+#     https://github.com/ScheindorfHyenetics/berrymedBluetoothOxymeter
+#
+# The sensor updates the readings at 100Hz.
+
+import time
+import adafruit_sdcard
+import board
+import busio
+import digitalio
+import storage
+import adafruit_pcf8523
+import _bleio
+import adafruit_ble
+from adafruit_ble.advertising.standard import Advertisement
+from adafruit_ble.services.standard.device_info import DeviceInfoService
+from adafruit_ble_berrymed_pulse_oximeter import BerryMedPulseOximeterService
+
+# Logging setup
+SD_CS = board.D10
+spi = busio.SPI(board.SCK, board.MOSI, board.MISO)
+cs = digitalio.DigitalInOut(SD_CS)
+sd_card = adafruit_sdcard.SDCard(spi, cs)
+vfs = storage.VfsFat(sd_card)
+storage.mount(vfs, "/sd_card")
+
+log_interval = 2  # you can adjust this to log at a different rate
+
+# RTC setup
+I2C = busio.I2C(board.SCL, board.SDA)
+rtc = adafruit_pcf8523.PCF8523(I2C)
+
+days = ("Sunday", "Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday")
+
+set_time = False
+if set_time:  # change to True if you want to write the time!
+    #             year, mon, date, hour, min, sec, wday, yday, isdst
+    t = time.struct_time((2020, 4, 21, 18, 13, 0, 2, -1, -1))
+    # you must set year, mon, date, hour, min, sec and weekday
+    # yearday  not supported, isdst can be set but we don't use it at this time
+    print("Setting time to:", t)  # uncomment for debugging
+    rtc.datetime = t
+    print()
+
+# PyLint can't find BLERadio for some reason so special case it here.
+ble = adafruit_ble.BLERadio()  # pylint: disable=no-member
+
+pulse_ox_connection = None
+
+while True:
+    t = rtc.datetime
+    print("Scanning for Pulse Oximeter...")
+    for adv in ble.start_scan(Advertisement, timeout=5):
+        name = adv.complete_name
+        if not name:
+            continue
+        # "BerryMed" devices may have trailing nulls on their name.
+        if name.strip("\x00") == "BerryMed":
+            pulse_ox_connection = ble.connect(adv)
+            print("Connected")
+            break
+
+    # Stop scanning whether or not we are connected.
+    ble.stop_scan()
+    print("Stopped scan")
+
+    try:
+        if pulse_ox_connection and pulse_ox_connection.connected:
+            print("Fetch connection")
+            if DeviceInfoService in pulse_ox_connection:
+                dis = pulse_ox_connection[DeviceInfoService]
+                try:
+                    manufacturer = dis.manufacturer
+                except AttributeError:
+                    manufacturer = "(Manufacturer Not specified)"
+                try:
+                    model_number = dis.model_number
+                except AttributeError:
+                    model_number = "(Model number not specified)"
+                print("Device:", manufacturer, model_number)
+            else:
+                print("No device information")
+
+            pulse_ox_service = pulse_ox_connection[BerryMedPulseOximeterService]
+
+            while pulse_ox_connection.connected:
+                values = pulse_ox_service.values
+                if values is not None:
+                    # unpack the message to 'values' list
+                    valid, spo2, pulse_rate, pleth, finger = values
+                    if not valid:
+                        continue
+                    if (
+                            pulse_rate == 255
+                    ):  # device sends 255 as pulse until it has a valid read
+                        continue
+                    print(
+                        "SpO2: {}%  | ".format(spo2),
+                        "Pulse Rate: {} BPM  | ".format(pulse_rate),
+                        "Pleth: {}".format(pleth),
+                    )
+                    # print((pleth,))  # uncomment to see graph on Mu plotter
+
+                    try:  # logging to SD card
+                        with open("/sd_card/log.txt", "a") as sdc:
+                            t = rtc.datetime
+                            sdc.write(
+                                "{} {}/{}/{} {}:{}:{} ".format(
+                                    days[t.tm_wday],
+                                    t.tm_mday,
+                                    t.tm_mon,
+                                    t.tm_year,
+                                    t.tm_hour,
+                                    t.tm_min,
+                                    t.tm_sec
+                                )
+                            )
+                            sdc.write(
+                                "{}, {}, {:.2f}\n".format(
+                                    spo2, pulse_rate, pleth
+                                )
+                            )
+
+                            time.sleep(log_interval)
+                    except OSError:
+                        pass
+                    except RuntimeError:
+                        pass
+    except _bleio.ConnectionError:
+        try:
+            pulse_ox_connection.disconnect()
+        except _bleio.ConnectionError:
+            pass
+        pulse_ox_connection = None