Merge pull request #71 from James-Mc1ntyre/master

Added recording class for Nonin 3231 device, to work with the cardiocieption HRD task

Author: micahgallen

systole/recording.py

@@ -748,3 +748,172 @@ def read(self, duration):
     def close(self):
         """Close TCPIP connections"""
         self.con.close()
+
+
+
+
+
+class Nonin3231USB:
+    """Recording Nonin 3231 USB HR signal through USB connection
+
+    Parameters
+    ----------
+    
+    serial : pySerial object
+        The `serial` instance interfacing with the USB port.
+        
+
+    Examples
+    --------
+    First, you will need to define a :py:func:`serial` instance, indexing the
+    USB port where the Nonin 3231 Pulse Oximeter is plugged.
+
+    >>> import serial
+    >>> ser = serial.Serial('COM4')
+
+    This instance is then used to create an :py:func:`Nonin3231USB` instance
+    that will be used for the recording from a Nonin 3231 USB device.
+
+    >>> from ecg.recording import Nonin3231USB
+    >>> exg = Nonin3231USB(serial).read(30)
+
+    Use the :py:func:`read` method to record some signal and save it in the
+    `exg` dictionary.
+
+    .. warning:: The signals received fom the host are appened to a list. This
+       process can require more time at each iteration as the signal length
+       increase in memory. You should alway make sure that this will not
+       interfer with other task and regularly save intermediate recording to
+       save resources.
+
+    Notes
+    -----
+    """
+
+    def __init__(
+        self,
+        serial,
+        add_channels: Optional[int] = 1,
+    ):
+        self.reset(serial, add_channels)
+
+    def reset(
+        self,
+        serial,
+        add_channels: Optional[int] = 1,
+    ):
+        """Initialize/restart the recording instance.
+
+        Parameters
+        ----------
+        serial : pySerial object
+            The `serial` instance interfacing with the USB port.
+
+        Returns
+        -------
+        Nonin3231USB instance.
+        """
+        self.serial = serial
+
+        # Initialize recording with empty lists
+        self.recording: List[float] = []
+        self.bpm: List[float] = []
+        self.SpO2: List[float] = []
+        self.times: List[float] = []
+        self.n_channels: Optional[int] = add_channels
+        if add_channels is not None:
+            self.channels: Optional[Dict[str, List]] = {}
+            for i in range(add_channels):
+                self.channels[f"Channel_{i}"] = []
+        else:
+            self.channels = None
+        
+        # print('channels: '+str(self.channels))
+
+        return self
+    
+    def setup(self):
+        self.reset(
+            serial=self.serial,
+        )
+
+        return self
+    
+    def read(self, duration: float):
+        """Read PPG signal for some amount of time.
+
+        Parameters
+        ----------
+        duration : int or float
+            Length of the desired recording time.
+        """
+        # init start ime
+        tstart = time.time()
+        
+        # read for length of duration 
+        while time.time() - tstart < duration:
+            # assert one full line of data is there
+            if self.serial.inWaiting() >= 12:
+                # Store line of data 
+                data = list(self.serial.readline())
+                # assert full data line
+                if len(data) < 12: 
+                    continue
+                # get bpm reading 
+                self.bpm.append(data[8])
+                # give bpm to recording as well
+                self.recording.append(data[8])
+                # get SpO2 reading (we don't use it)
+                self.SpO2.append(data[6])
+                # get 'time' reading (seconds) 
+                self.times.append(data[5])
+                # Add 0 to the additional channels
+                if self.channels is not None:
+                    for ch in self.channels:
+                        self.channels[ch].append(0)
+        
+        return self
+    
+    
+    def readInWaiting(self, bool = False):
+        """Read in waiting Nonin data.
+
+        Parameters
+        ----------
+        stop : bool
+            Stop the recording when an error is detected. Default is *False*.
+        """
+
+        #  nonin device reads out 12 bits per message
+        while self.serial.inWaiting() >= 12:
+
+            # Store full message line
+            data = list(self.serial.readline())
+            # assert that there is a full line of data
+            if len(data) < 12: 
+                continue
+            # get bpm reading 
+            self.bpm.append(data[8])
+            # give bpm to recording as well
+            self.recording.append(data[8])
+            # get SpO2 reading (we don't use it)
+            self.SpO2.append(data[6])
+            # get 'time' reading (seconds) 
+            self.times.append(data[5])
+            # Add 0 to the additional channels for triggers
+            if self.channels is not None:
+                for ch in self.channels:
+                    self.channels[ch].append(0)
+        
+
+    
+    def save(self, fname: str):
+        """
+        Not saving the data as of now, only results
+        """
+        None
+
+    
+    def close(self):
+        """Close serial connections"""
+        self.serial.close()