InfiniTime.git

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292

#include "components/heartrate/Ppg.h"
#include <nrf_log.h>
#include <vector>

using namespace Pinetime::Controllers;

namespace {
  float LinearInterpolation(const float* xValues, const float* yValues, int length, float pointX) {
    if (pointX > xValues[length - 1]) {
      return yValues[length - 1];
    } else if (pointX <= xValues[0]) {
      return yValues[0];
    }
    int index = 0;
    while (pointX > xValues[index] && index < length - 1) {
      index++;
    }
    float pointX0 = xValues[index - 1];
    float pointX1 = xValues[index];
    float pointY0 = yValues[index - 1];
    float pointY1 = yValues[index];
    float mu = (pointX - pointX0) / (pointX1 - pointX0);

    return (pointY0 * (1 - mu) + pointY1 * mu);
  }

  float PeakSearch(float* xVals, float* yVals, float threshold, float& width, float start, float end, int length) {
    int peaks = 0;
    bool enabled = false;
    float minBin = 0.0f;
    float maxBin = 0.0f;
    float peakCenter = 0.0f;
    float prevValue = LinearInterpolation(xVals, yVals, length, start - 0.01f);
    float currValue = LinearInterpolation(xVals, yVals, length, start);
    float idx = start;
    while (idx < end) {
      float nextValue = LinearInterpolation(xVals, yVals, length, idx + 0.01f);
      if (currValue < threshold) {
        enabled = true;
      }
      if (currValue >= threshold and enabled) {
        if (prevValue < threshold) {
          minBin = idx;
        } else if (nextValue <= threshold) {
          maxBin = idx;
          peaks++;
          width = maxBin - minBin;
          peakCenter = width / 2.0f + minBin;
        }
      }
      prevValue = currValue;
      currValue = nextValue;
      idx += 0.01f;
    }
    if (peaks != 1) {
      width = 0.0f;
      peakCenter = 0.0f;
    }
    return peakCenter;
  }

  float SpectrumMean(const std::array<float, Ppg::spectrumLength>& signal, int start, int end) {
    int total = 0;
    float mean = 0.0f;
    for (int idx = start; idx < end; idx++) {
      mean += signal.at(idx);
      total++;
    }
    if (total > 0) {
      mean /= static_cast<float>(total);
    }
    return mean;
  }

  float SignalToNoise(const std::array<float, Ppg::spectrumLength>& signal, int start, int end, float max) {
    float mean = SpectrumMean(signal, start, end);
    return max / mean;
  }

  // Simple bandpass filter using exponential moving average
  void Filter30to240(std::array<float, Ppg::dataLength>& signal) {
    // From:
    // https://www.norwegiancreations.com/2016/03/arduino-tutorial-simple-high-pass-band-pass-and-band-stop-filtering/

    int length = signal.size();
    // 0.268 is ~0.5Hz and 0.816 is ~4Hz cutoff at 10Hz sampling
    float expAlpha = 0.816f;
    float expAvg = 0.0f;
    for (int loop = 0; loop < 4; loop++) {
      expAvg = signal.front();
      for (int idx = 0; idx < length; idx++) {
        expAvg = (expAlpha * signal.at(idx)) + ((1 - expAlpha) * expAvg);
        signal[idx] = expAvg;
      }
    }
    expAlpha = 0.268f;
    for (int loop = 0; loop < 4; loop++) {
      expAvg = signal.front();
      for (int idx = 0; idx < length; idx++) {
        expAvg = (expAlpha * signal.at(idx)) + ((1 - expAlpha) * expAvg);
        signal[idx] -= expAvg;
      }
    }
  }

  float SpectrumMax(const std::array<float, Ppg::spectrumLength>& data, int start, int end) {
    float max = 0.0f;
    for (int idx = start; idx < end; idx++) {
      if (data.at(idx) > max) {
        max = data.at(idx);
      }
    }
    return max;
  }

  void Detrend(std::array<float, Ppg::dataLength>& signal) {
    int size = signal.size();
    float offset = signal.front();
    float slope = (signal.at(size - 1) - offset) / static_cast<float>(size - 1);

    for (int idx = 0; idx < size; idx++) {
      signal[idx] -= (slope * static_cast<float>(idx) + offset);
    }
    for (int idx = 0; idx < size - 1; idx++) {
      signal[idx] = signal[idx + 1] - signal[idx];
    }
  }

  // Hanning Coefficients from numpy: python -c 'import numpy;print(numpy.hanning(64))'
  // Note: Harcoded and must be updated if constexpr dataLength is changed. Prevents the need to
  // use cosf() which results in an extra ~5KB in storage.
  // This data is symetrical so just using the first half (saves 128B when dataLength is 64).
  static constexpr float hanning[Ppg::dataLength >> 1] {
    0.0f,        0.00248461f, 0.00991376f, 0.0222136f,  0.03926189f, 0.06088921f, 0.08688061f, 0.11697778f,
    0.15088159f, 0.1882551f,  0.22872687f, 0.27189467f, 0.31732949f, 0.36457977f, 0.41317591f, 0.46263495f,
    0.51246535f, 0.56217185f, 0.61126047f, 0.65924333f, 0.70564355f, 0.75f,       0.79187184f, 0.83084292f,
    0.86652594f, 0.89856625f, 0.92664544f, 0.95048443f, 0.96984631f, 0.98453864f, 0.99441541f, 0.99937846f};
}

Ppg::Ppg() {
  dataAverage.fill(0.0f);
  spectrum.fill(0.0f);
}

int8_t Ppg::Preprocess(uint32_t hrs, uint32_t als) {
  if (dataIndex < dataLength) {
    dataHRS[dataIndex++] = hrs;
  }
  alsValue = als;
  if (alsValue > alsThreshold) {
    return 1;
  }
  return 0;
}

int Ppg::HeartRate() {
  if (dataIndex < dataLength) {
    return 0;
  }
  int hr = 0;
  hr = ProcessHeartRate(resetSpectralAvg);
  resetSpectralAvg = false;
  // Make room for overlapWindow number of new samples
  for (int idx = 0; idx < dataLength - overlapWindow; idx++) {
    dataHRS[idx] = dataHRS[idx + overlapWindow];
  }
  dataIndex = dataLength - overlapWindow;
  return hr;
}

void Ppg::Reset(bool resetDaqBuffer) {
  if (resetDaqBuffer) {
    dataIndex = 0;
  }
  avgIndex = 0;
  dataAverage.fill(0.0f);
  lastPeakLocation = 0.0f;
  alsThreshold = UINT16_MAX;
  alsValue = 0;
  resetSpectralAvg = true;
  spectrum.fill(0.0f);
}

// Pass init == true to reset spectral averaging.
// Returns -1 (Reset Acquisition), 0 (Unable to obtain HR) or HR (BPM).
int Ppg::ProcessHeartRate(bool init) {
  std::copy(dataHRS.begin(), dataHRS.end(), vReal.begin());
  Detrend(vReal);
  Filter30to240(vReal);
  vImag.fill(0.0f);
  // Apply Hanning Window
  int hannIdx = 0;
  for (int idx = 0; idx < dataLength; idx++) {
    if (idx >= dataLength >> 1) {
      hannIdx--;
    }
    vReal[idx] *= hanning[hannIdx];
    if (idx < dataLength >> 1) {
      hannIdx++;
    }
  }
  // Compute in place power spectrum
  ArduinoFFT<float> FFT = ArduinoFFT<float>(vReal.data(), vImag.data(), dataLength, sampleFreq);
  FFT.compute(FFTDirection::Forward);
  FFT.complexToMagnitude();
  FFT.~ArduinoFFT();
  SpectrumAverage(vReal.data(), spectrum.data(), spectrum.size(), init);
  peakLocation = 0.0f;
  float threshold = peakDetectionThreshold;
  float peakWidth = 0.0f;
  int specLen = spectrum.size();
  float max = SpectrumMax(spectrum, hrROIbegin, hrROIend);
  float signalToNoiseRatio = SignalToNoise(spectrum, hrROIbegin, hrROIend, max);
  if (signalToNoiseRatio > signalToNoiseThreshold && spectrum.at(0) < dcThreshold) {
    threshold *= max;
    // Reuse VImag for interpolation x values passed to PeakSearch
    for (int idx = 0; idx < dataLength; idx++) {
      vImag[idx] = idx;
    }
    peakLocation = PeakSearch(vImag.data(),
                              spectrum.data(),
                              threshold,
                              peakWidth,
                              static_cast<float>(hrROIbegin),
                              static_cast<float>(hrROIend),
                              specLen);
    peakLocation *= freqResolution;
  }
  // Peak too wide? (broad spectrum noise or large, rapid HR change)
  if (peakWidth > maxPeakWidth) {
    peakLocation = 0.0f;
  }
  // Check HR limits
  if (peakLocation < minHR || peakLocation > maxHR) {
    peakLocation = 0.0f;
  }
  // Reset spectral averaging if bad reading
  if (peakLocation == 0.0f) {
    resetSpectralAvg = true;
  }
  // Set the ambient light threshold and return HR in BPM
  alsThreshold = static_cast<uint16_t>(alsValue * alsFactor);
  // Get current average HR. If HR reduced to zero, return -1 (reset) else HR
  peakLocation = HeartRateAverage(peakLocation);
  int rtn = -1;
  if (peakLocation == 0.0f && lastPeakLocation > 0.0f) {
    lastPeakLocation = 0.0f;
  } else {
    lastPeakLocation = peakLocation;
    rtn = static_cast<int>((peakLocation * 60.0f) + 0.5f);
  }
  return rtn;
}

void Ppg::SpectrumAverage(const float* data, float* spectrum, int length, bool reset) {
  if (reset) {
    spectralAvgCount = 0;
  }
  float count = static_cast<float>(spectralAvgCount);
  for (int idx = 0; idx < length; idx++) {
    spectrum[idx] = (spectrum[idx] * count + data[idx]) / (count + 1);
  }
  if (spectralAvgCount < spectralAvgMax) {
    spectralAvgCount++;
  }
}

float Ppg::HeartRateAverage(float hr) {
  avgIndex++;
  avgIndex %= dataAverage.size();
  dataAverage[avgIndex] = hr;
  float avg = 0.0f;
  float total = 0.0f;
  float min = 300.0f;
  float max = 0.0f;
  for (const float& value : dataAverage) {
    if (value > 0.0f) {
      avg += value;
      if (value < min)
        min = value;
      if (value > max)
        max = value;
      total++;
    }
  }
  if (total > 0) {
    avg /= total;
  } else {
    avg = 0.0f;
  }
  return avg;
}