189 lines
4.8 KiB
Python
189 lines
4.8 KiB
Python
# SPDX-License-Identifier: LGPL-3.0-or-later
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# Copyright (C) 2020 Daniel Thompson
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"""Photoplethysmogram (PPG) Signal Processing
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Algorithms and signal processing primatives that can be used to convert
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raw PPG signals into something useful.
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"""
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import array
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import micropython
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import watch
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@micropython.viper
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def _compare(d1, d2, count: int, shift: int) -> int:
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"""Compare two sequences of (signed) bytes and quantify how dissimilar
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they are.
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"""
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p1 = ptr8(d1)
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p2 = ptr8(d2)
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e = 0
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for i in range(count):
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s1 = int(p1[i])
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if s1 > 127:
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s1 -= 256
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s2 = int(p2[i])
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if s2 > 127:
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s2 -= 256
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d = s1 - s2
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e += d*d
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return e
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class Biquad():
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"""Direct Form II Biquad Filter"""
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def __init__(self, b0, b1, b2, a1, a2):
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self._coeff = (b0, b1, b2, a1, a2)
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self._v1 = 0
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self._v2 = 0
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def step(self, x):
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c = self._coeff
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v1 = self._v1
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v2 = self._v2
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v = x - (c[3] * v1) - (c[4] * v2)
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y = (c[0] * v) + (c[1] * v1) + (c[2] * v2)
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self._v2 = v1
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self._v1 = v
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return y
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class PTAGC():
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"""Peak Tracking Automatic Gain Control
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In order for the correlation checks to work correctly we must
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aggressively reject spikes caused by fast DC steps. Setting a
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threshold based on the median is very effective at killing
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spikes but needs an extra 1k for sample storage which isn't
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really plausible for a microcontroller.
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"""
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def __init__(self, start, decay, threshold):
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self._peak = start
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self._decay = decay
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self._boost = 1 / decay
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self._threshold = threshold
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def step(self, spl):
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# peak tracking
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peak = self._peak
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if abs(spl) > peak:
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peak *= self._boost
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else:
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peak *= self._decay
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self._peak = peak
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# rejection filter (clipper)
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threshold = self._threshold
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if spl > (peak * threshold) or spl < (peak * -threshold):
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return 0
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# booster
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spl = 100 * spl / (2 * peak)
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return spl
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class PPG():
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"""
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"""
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def __init__(self, spl):
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self._offset = spl
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self.data = array.array('b')
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self.debug = None
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self._hpf = Biquad(0.87033078, -1.74066156, 0.87033078,
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-1.72377617, 0.75754694)
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self._agc = PTAGC(20, 0.971, 2)
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self._lpf = Biquad(0.11595249, 0.23190498, 0.11595249,
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-0.72168143, 0.18549138)
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def preprocess(self, spl):
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"""Preprocess a PPG sample.
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Must be called at 24Hz for accurate heart rate calculations.
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"""
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if self.debug != None:
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self.debug.append(spl)
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spl -= self._offset
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spl = self._hpf.step(spl)
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spl = self._agc.step(spl)
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spl = self._lpf.step(spl)
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spl = int(spl)
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self.data.append(spl)
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return spl
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def _get_heart_rate(self):
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def compare(d, shift):
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return _compare(d[shift:], d[:-shift], len(d)-shift, shift)
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def trough(d, mn, mx):
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z2 = compare(d, mn-2)
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z1 = compare(d, mn-1)
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for i in range(mn, mx+1):
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z = compare(d, i)
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if z2 > z1 and z1 < z:
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return i
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z2 = z1
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z1 = z
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return -1
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data = memoryview(self.data)
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# Search initially from ~210 to 30 bpm
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t0 = trough(data, 7, 48)
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if t0 < 0:
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return None
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# Check the second cycle ...
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t1 = t0 * 2
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t1 = trough(data, t1 - 5, t1 + 5)
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if t1 < 0:
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return None
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# ... and the third
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t2 = (t1 * 3) // 2
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t2 = trough(data, t2 - 5, t2 + 4)
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if t2 < 0:
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return None
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# If we can find a fourth cycle then use that for the extra
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# precision otherwise report whatever we've found
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t3 = (t2 * 4) // 3
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t3 = trough(data, t3 - 4, t3 + 4)
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if t3 < 0:
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return (60 * 24 * 3) // t2
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return (60 * 24 * 4) // t3
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def get_heart_rate(self):
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if len(self.data) < 200:
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return None
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hr = self._get_heart_rate()
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# Clear out the accumulated data
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self.data = array.array('b')
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# Dump the debug data
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if self.debug:
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with open('hrs.data', 'ab') as f:
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# Re-sync marker
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f.write(b'\xff\xff')
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now = watch.rtc.get_localtime()
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f.write(array.array('H', now[:6]))
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f.write(self.debug)
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self.debug = array.array('H')
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return hr
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def enable_debug(self):
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if self.debug == None:
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self.debug = array.array('H')
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