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Merge pull request #124 from syoung-smallwisdom/update-algo
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Update algorithms to match iOS implementation
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@syoung-smallwisdom
syoung-smallwisdom committed May 1, 2019
2 parents ddc125c + b285dd7 commit 6590467
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15 changes: 11 additions & 4 deletions crf/src/main/java/org/sagebase/crf/step/active/HeartRateSampleProcessor.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ val SUPPORTED_FRAME_RATES = arrayOf(30)
/// The number of seconds for the window used to calculate the heart rate.
const val HEART_RATE_WINDOW_IN_SECONDS: Double = 10.0
const val HEART_RATE_MIN_FRAME_RATE: Double = 12.0
const val HEART_RATE_FILTER_DROP_IN_SECONDS: Double = 2.0

const val HEART_RATE_MAX: Double = 210.0
const val HEART_RATE_MIN: Double = 45.0
Expand Down Expand Up @@ -79,7 +80,7 @@ class HeartRateSampleProcessor @JvmOverloads constructor(val videoProcessorFrame
// look to see if we have enough to process a bpm
// Need to keep 2 extra seconds due to filtering lopping off the first 2 seconds of data.
val meanOrder = meanFilterOrder(roundedRate)
val windowLength = (HEART_RATE_WINDOW_IN_SECONDS + 2).roundToInt() * roundedRate + meanOrder
val windowLength = (HEART_RATE_WINDOW_IN_SECONDS + 2.0 * HEART_RATE_FILTER_DROP_IN_SECONDS).roundToInt() * roundedRate + meanOrder

return (pixelSamples.size >= windowLength)
}
Expand Down Expand Up @@ -302,13 +303,19 @@ class HeartRateSampleProcessor @JvmOverloads constructor(val videoProcessorFrame
// (because the 3 seconds is removed by checking for the isLensCovered flag), but to match his output
// it is reproduced here for testing purposes.
val drop = if (dropSeconds > 0) dropSeconds * samplingRate - 1 else 0
val x = input.drop(drop).map { if (it.isFinite()) it else 0.0 }

// get minimum value in the input window and offset each signal frame by the minimum value observed in the window
// let minValue = x.min()
// let minnedOutX = x.map({$0 - minValue!})
val xInput = input.drop(drop)
val minValue = xInput.min() ?: 0.0
val x = xInput.map { if (it.isFinite()) (it - minValue) else 0.0 }
// x <- signal::filter(bf_low, x) # lowpass
// x <- x[round(sampling_rate):length(x)] # 1s
val lowpass = passFilter(x.toDoubleArray(), samplingRate = samplingRate, type = FilterType.low).drop(samplingRate)
val lowpass = passFilter(x.toDoubleArray(), samplingRate = samplingRate, type = FilterType.low).drop(HEART_RATE_FILTER_DROP_IN_SECONDS.toInt() * samplingRate)
// x <- signal::filter(bf_high, x) # highpass
// x <- x[round(sampling_rate):length(x)] # 1s @ 60Hz
val highpass = passFilter(lowpass.toDoubleArray(), samplingRate = samplingRate, type = FilterType.high).drop(samplingRate)
val highpass = passFilter(lowpass.toDoubleArray(), samplingRate = samplingRate, type = FilterType.high).drop(HEART_RATE_FILTER_DROP_IN_SECONDS.toInt() * samplingRate)
// filter using mean centering
val filtered = meanCenteringFilter(highpass.toDoubleArray(), samplingRate = samplingRate)
return filtered
Expand Down
148 changes: 37 additions & 111 deletions crf/src/test/java/org/sagebase/crf/step/active/HeartRateSampleProcessorTest.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -168,31 +168,6 @@ class HeartRateSampleProcessorTest {
assertEquals(65, processor.meanFilterOrder(60))
}

@Test
fun testGetFilteredSignal_Red() {
val processor = HeartRateSampleProcessor()
val testHRData = testHRData()

val input = testHRData.hr_data.map { it.red }
val samplingRate = 60
val expectedOutput = testHRData.hr_data_filtered.map { it.red }.toDoubleArray()
val output = processor.getFilteredSignal(input, samplingRate, 3)
compare(expectedOutput, output, 0.0001)
}

@Test
fun testGetFilteredSignal_Green() {
val processor = HeartRateSampleProcessor()
val testHRData = testHRData()

val input = testHRData.hr_data.map { it.green }
val samplingRate = 60
val expectedOutput = testHRData.hr_data_filtered.map { it.green }.toDoubleArray()
val output = processor.getFilteredSignal(input, samplingRate, 3)
compare(expectedOutput, output, 0.0001)
}


@Test
fun testCalculatedLag() {
val processor = HeartRateSampleProcessor()
Expand All @@ -204,21 +179,6 @@ class HeartRateSampleProcessorTest {
assertEquals(testData.maxLag(), maxLag)
}

@Test
fun testChunkedSamples() {
val processor = HeartRateSampleProcessor()
val testHRData = testHRData()

val samplingRate = processor.calculateSamplingRate(testHRData.hr_data.toList())
val input = testHRData.hr_data_filtered.map { it.red }
val expectedOutput = testHRData.flip(testHRData.hr_data_filtered_chunked.red)
val output = processor.chunkSamples(input, samplingRate)
assertEquals(output.size, expectedOutput.size)
for (ii in 0 until output.size) {
compare(output[ii], expectedOutput[ii], 0.00000001)
}
}

@Test
fun testEarlierPeaks() {
val processor = HeartRateSampleProcessor()
Expand Down Expand Up @@ -291,8 +251,9 @@ class HeartRateSampleProcessorTest {
val testHRData = testHRData()

val samplingRate = processor.calculateSamplingRate(testHRData.hr_data.toList())
val roundedRate = samplingRate.roundToInt()

val inputChunks: Array<DoubleArray> = testHRData.flip(testHRData.hr_data_filtered_chunked.red)
val inputChunks: Array<DoubleArray> = testHRData.flip(testHRData.hr_data_chunks.red)
val expectedOutputs: Array<HRTuple> = testHRData.hr_estimates.red

// check assumption
Expand All @@ -301,11 +262,13 @@ class HeartRateSampleProcessorTest {
// Only check some of the results b/c the calculations are for a resting heart rate and all use
// initial estimate or else they are invalid (Initial windows).
for (ii in 0 until Math.min(10, expectedOutputs.size)) {
val (hr, confidence) = processor.calculateHRFromFilteredSamples(inputChunks[ii], samplingRate)
//let filteredData = processor.getFilteredSignal(inputChunks[ii], samplingRate: roundedSamplingRate)
val filteredData = processor.getFilteredSignal(inputChunks[ii].toList(), roundedRate)
val (hr, confidence) = processor.calculateHRFromFilteredSamples(filteredData, samplingRate)
val expectedHR = expectedOutputs[ii].hr
val expectedConfidence = expectedOutputs[ii].confidence
assertEquals(expectedHR, hr,0.000001)
assertEquals(expectedConfidence, confidence, 0.000001)
assertEquals(expectedHR, hr,0.0001)
assertEquals(expectedConfidence, confidence, 0.0001)
}
}

Expand All @@ -315,8 +278,9 @@ class HeartRateSampleProcessorTest {
val testHRData = testHRData()

val samplingRate = processor.calculateSamplingRate(testHRData.hr_data.toList())
val roundedRate = samplingRate.roundToInt()

val inputChunks: Array<DoubleArray> = testHRData.flip(testHRData.hr_data_filtered_chunked.green)
val inputChunks: Array<DoubleArray> = testHRData.flip(testHRData.hr_data_chunks.green)
val expectedOutputs: Array<HRTuple> = testHRData.hr_estimates.green

// check assumption
Expand All @@ -325,11 +289,12 @@ class HeartRateSampleProcessorTest {
// Only check some of the results b/c the calculations are for a resting heart rate and all use
// initial estimate or else they are invalid (Initial windows).
for (ii in 0 until Math.min(10, expectedOutputs.size)) {
val (hr, confidence) = processor.calculateHRFromFilteredSamples(inputChunks[ii], samplingRate)
val filteredData = processor.getFilteredSignal(inputChunks[ii].toList(), roundedRate)
val (hr, confidence) = processor.calculateHRFromFilteredSamples(filteredData, samplingRate)
val expectedHR = expectedOutputs[ii].hr
val expectedConfidence = expectedOutputs[ii].confidence
assertEquals(expectedHR, hr,0.000001)
assertEquals(expectedConfidence, confidence, 0.000001)
assertEquals(expectedHR, hr,0.0001)
assertEquals(expectedConfidence, confidence, 0.0001)
}
}

Expand All @@ -339,8 +304,9 @@ class HeartRateSampleProcessorTest {
val testHRData = testHRData12hz()

val samplingRate = processor.calculateSamplingRate(testHRData.hr_data.toList())
val roundedRate = samplingRate.roundToInt()

val inputChunks: Array<DoubleArray> = testHRData.flip(testHRData.hr_data_filtered_chunked.red)
val inputChunks: Array<DoubleArray> = testHRData.flip(testHRData.hr_data_chunks.red)
val expectedOutputs: Array<HRTuple> = testHRData.hr_estimates.red

// check assumption
Expand All @@ -349,56 +315,15 @@ class HeartRateSampleProcessorTest {
// Only check some of the results b/c the calculations are for a resting heart rate and all use
// initial estimate or else they are invalid (Initial windows).
for (ii in 0 until Math.min(10, expectedOutputs.size)) {
val (hr, confidence) = processor.calculateHRFromFilteredSamples(inputChunks[ii], samplingRate)
val filteredData = processor.getFilteredSignal(inputChunks[ii].toList(), roundedRate)
val (hr, confidence) = processor.calculateHRFromFilteredSamples(filteredData, samplingRate)
val expectedHR = expectedOutputs[ii].hr
val expectedConfidence = expectedOutputs[ii].confidence
assertEquals(expectedHR, hr,0.000001)
assertEquals(expectedConfidence, confidence, 0.000001)
}
}

@Test
fun testIsReadyToProcess() {

val processor = HeartRateSampleProcessor()
val testHRData = testHRData()
val estimatedSamplingRate = 60.0
val drop = (3.0 * estimatedSamplingRate).roundToInt() - 1
val samples = testHRData.hr_data.drop(drop)
val roundedRate = estimatedSamplingRate.roundToInt()

// Add samples less than 12 seconds + mean order (65)
val eleven = roundedRate * 11
processor.pixelSamples.addAll(samples.subList(0, eleven))
assertFalse(processor.isReadyToProcess())

// Add samples for 12 seconds + mean order
val nextChunk = eleven + roundedRate + 65
processor.pixelSamples.addAll(samples.subList(eleven, nextChunk))
assertTrue(processor.isReadyToProcess())
}

@Test
fun testIsReadyToProcess_12hz() {

val processor = HeartRateSampleProcessor()
val testHRData = testHRData12hz()
val estimatedSamplingRate = 12.728
val drop = (3.0 * estimatedSamplingRate).roundToInt() - 1
val samples = testHRData.hr_data.drop(drop)
val roundedRate = estimatedSamplingRate.roundToInt()

// Add samples less than 12 seconds
val eleven = roundedRate * 11
processor.pixelSamples.addAll(samples.subList(0, eleven))
assertFalse(processor.isReadyToProcess())

// Add samples for 12 seconds + mean order
val nextChunk = eleven + roundedRate + 15 + 1
processor.pixelSamples.addAll(samples.subList(eleven, nextChunk))
assertTrue(processor.isReadyToProcess())
}

@Test
fun testProcessSamples() {

Expand All @@ -410,31 +335,32 @@ class HeartRateSampleProcessorTest {
// only process a subset of the data. syoung 04/16/2019
val start = 30
val expectedHRValues = arrayOf<HeartRateBPM>(
HeartRateBPM(47.3040004163,69.27709332103974,0.8683590800933014,"green"),
HeartRateBPM(48.3046064583,67.96997857106084,0.8644802170884017,"green"),
HeartRateBPM(49.3052123743,69.27709376612277,0.8936955072357293,"green"),
HeartRateBPM(50.3058184583,67.96997813437561,0.9014633198345332,"green"),
HeartRateBPM(51.3064244993,67.9699768399158,0.9108713480292215,"green"),
HeartRateBPM(52.3070303743,67.96997748974505,0.9071506266991106,"green"),
HeartRateBPM(53.3076363743,67.96997792123159,0.9000145584327659,"green"),
HeartRateBPM(54.3082423743,67.96997792123162,0.8998513053646106,"green"),
HeartRateBPM(55.3088484993,67.96997727140241,0.9128580892467326,"green"),
HeartRateBPM(56.3094543333,67.96997792123159,0.9029084106060474,"green"),
HeartRateBPM(57.3100602913,67.96997792123162,0.89087079839508,"green"),
HeartRateBPM(58.3106662913,67.96997770288898,0.8793877599812155,"green"),
HeartRateBPM(59.3112722493,67.96997835791682,0.8893933827220402,"green"),
HeartRateBPM(60.3118782083,67.9699783527182,0.8879583462485395,"green"),
HeartRateBPM(61.3124843743,67.96997705825844,0.8743429841892499,"green")
HeartRateBPM(46.3200712493,69.26537857647685,0.8665728400250351,"green"),
HeartRateBPM(47.3206772493,69.26537781379395,0.864004456488016,"green"),
HeartRateBPM(48.3212832913,67.9584831399785,0.8768333193716425,"green"),
HeartRateBPM(49.3218892083,69.26537780919945,0.8797011803396284,"red"),
HeartRateBPM(50.3224952083,67.95848369894412,0.8994492066282034,"green"),
HeartRateBPM(51.3231009993,67.9584846410716,0.9115548708180149,"green"),
HeartRateBPM(52.3237071663,67.95848426692528,0.9090951134939645,"green"),
HeartRateBPM(53.3243131243,67.95848426692528,0.9016664647138142,"green"),
HeartRateBPM(54.3249191243,67.95848426692525,0.8985739988740599,"red"),
HeartRateBPM(55.3255251663,67.95848370345189,0.9095022749620564,"green"),
HeartRateBPM(56.3261310413,67.95848483039869,0.8958170645972368,"green"),
HeartRateBPM(57.3267370413,67.95848445174457,0.8956174838084865,"green"),
HeartRateBPM(58.3273430413,67.95848464107164,0.8986418987043391,"green"),
HeartRateBPM(59.3279491243,67.95848407759824,0.8896016693876465,"green"),
HeartRateBPM(60.3285551243,67.9584840775982,0.8895332581586164,"green"),
HeartRateBPM(61.3291610833,67.9584836989441,0.8901171128383659,"red")
)

val drop = (3.0 * estimatedSamplingRate).roundToInt() - 1 + (start * estimatedSamplingRate).roundToInt()
val drop = (start * estimatedSamplingRate).roundToInt()
val samples = testHRData.hr_data.drop(drop)
var expectedIdx = 0

// Test expectations to see that they match the Swift implementation
assertEquals(1979, drop)
assertEquals(1681, samples.size)
assertEquals(34.2294156243, samples.first().timestamp, 0.0000001)
assertEquals(1800, drop)
assertEquals(1860, samples.size)
assertEquals(31.2442744993, samples.first().timestamp, 0.0000001)

samples.forEach {
processor.addSample(it)
Expand Down
4 changes: 1 addition & 3 deletions crf/src/test/java/org/sagebase/crf/step/active/HeartRateTestDataLoader.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -144,9 +144,7 @@ class HeartRateTestDataLoader {

data class HRProcessorTestData(
var hr_data : Array<TestPixelSample>,
var hr_data_filtered : Array<ColorData>,
var hr_data_filtered_chunked : ColorDataChunked,
var hr_data_filtered_chunked_acf : ColorDataChunked,
var hr_data_chunks : ColorDataChunked,
var hr_estimates : HrEstimates
) {

Expand Down
2 changes: 1 addition & 1 deletion crf/src/test/resources/io_examples_whole.json
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2 changes: 1 addition & 1 deletion crf/src/test/resources/io_examples_whole_12hz.json
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