ppg: Pull the PPG signal processing into a seperate library

Signed-off-by: Daniel Thompson <daniel@redfelineninja.org.uk>

1 files changed, 9 insertions, 127 deletions

diff --git a/wasp/apps/heart.py b/wasp/apps/heart.py
index fdf8336..367d17a 100644
--- a/wasp/apps/heart.py
+++ b/wasp/apps/heart.py
@@ -2,112 +2,8 @@
 # Copyright (C) 2020 Daniel Thompson
 
 import wasp
-import array
 import machine
-
-class Biquad():
-    """Direct Form II Biquad Filter"""
-
-    def __init__(self, b0, b1, b2, a1, a2):
-        self._coeff = (b0, b1, b2, a1, a2)
-        self._v1 = 0
-        self._v2 = 0
-
-    def step(self, x):
-        c = self._coeff
-        v1 = self._v1
-        v2 = self._v2
-
-        v = x - (c[3] * v1) - (c[4] * v2)
-        y = (c[0] * v) + (c[1] * v1) + (c[2] * v2)
-
-        self._v2 = v1
-        self._v1 = v
-        return y
-
-class PTAGC():
-    """Peak Tracking Automatic Gain Control
-
-    In order for the correlation checks to work correctly we must
-    aggressively reject spikes caused by fast DC steps. Setting a
-    threshold based on the median is very effective at killing
-    spikes but needs an extra 1k for sample storage which isn't
-    really plausible for a microcontroller.
-    """
-    def __init__(self, start, decay, threshold):
-        self._peak = start
-        self._decay = decay
-        self._boost = 1 / decay
-        self._threshold = threshold
-
-    def step(self, spl):
-        # peak tracking
-        peak = self._peak
-        if abs(spl) > peak:
-            peak *= self._boost
-        else:
-            peak *= self._decay
-        self._peak = peak
-
-        # rejection filter (clipper)
-        threshold = self._threshold
-        if spl > (peak * threshold) or spl < (peak * -threshold):
-            return 0
-
-        # booster
-        spl = 100 * spl / (2 * peak)
-
-        return spl
-
-def _compare(d1, d2, count, shift):
-    e = 0
-    for i in range(count):
-        d = d1[i] - d2[i]
-        e += d*d
-    return e
-
-def compare(d, shift):
-    return _compare(d[shift:], d[:-shift], len(d)-shift, shift)
-
-def trough(d, mn, mx):
-    z2 = compare(d, mn-2)
-    z1 = compare(d, mn-1)
-    for i in range(mn, mx+1):
-        z = compare(d, i)
-        if z2 > z1 and z1 < z:
-            return i
-        z2 = z1
-        z1 = z
-
-    return -1
-
-def get_hrs(d):
-    din = memoryview(d)
-
-    # Search initially from ~210 to 30 bpm
-    t0 = trough(din, 7, 48)
-    if t0 < 0:
-        return None
-
-    # Check the second cycle ...
-    t1 = t0 * 2
-    t1 = trough(din, t1 - 5, t1 + 5)
-    if t1 < 0:
-        return None
-
-    # ... and the third
-    t2 = (t1 * 3) // 2
-    t2 = trough(din, t2 - 5, t2 + 4)
-    if t2 < 0:
-        return None
-
-    # If we can find a fourth cycle then use that for the extra
-    # precision otherwise report whatever we've found
-    t3 = (t2 * 4) // 3
-    t3 = trough(din, t3 - 4, t3 + 4)
-    if t3 < 0:
-        return (60 * 24 * 3) // t2
-    return (60 * 24 * 4) // t3
+import ppg
 
 class HeartApp():
     """Heart Rate Sensing application.
@@ -125,40 +21,26 @@ class HeartApp():
         draw.fill()
         draw.string('PPG graph', 0, 6, width=240)
 
-        self._hpf = Biquad(0.87033078, -1.74066156, 0.87033078, -1.72377617, 0.75754694)
-        self._agc = PTAGC(20, 0.971, 2)
-        self._lpf = Biquad(0.11595249, 0.23190498, 0.11595249, -0.72168143, 0.18549138)
+        wasp.system.request_tick(1000 // 8)
 
+        self._hrdata = ppg.PPG(wasp.watch.hrs.read_hrs())
         self._x = 0
-        self._offset = wasp.watch.hrs.read_hrs()
-
-        self._hrdata = array.array('b')
-
-        wasp.system.request_tick(1000 // 8)
 
     def background(self):
         wasp.watch.hrs.disable()
-        del self._hpf
-        del self._agc
-        del self._lpf
+        del self._hrdata
 
     def _subtick(self, ticks):
         """Notify the application that its periodic tick is due."""
         draw = wasp.watch.drawable
 
-        spl = wasp.watch.hrs.read_hrs()
-        spl -= self._offset
-        spl = self._hpf.step(spl)
-        spl = self._agc.step(spl)
-        spl = self._lpf.step(spl)
-        spl = int(spl)
+        spl = self._hrdata.preprocess(wasp.watch.hrs.read_hrs())
 
-        self._hrdata.append(spl)
-        if len(self._hrdata) >= 240:
-            draw.string('{} bpm'.format(get_hrs(self._hrdata)), 0, 6, width=240)
-            del self._hrdata
-            self._hrdata = array.array('b')
+        if len(self._hrdata.data) >= 240:
+            draw.string('{} bpm'.format(self._hrdata.get_heart_rate()),
+                        0, 6, width=240)
 
+        # Graph is orange by default...
         color = 0xffc0
 
         # If the maths goes wrong lets show it in the chart!