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Fixed an issue with troughs being labelled as peaks #320
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@cathieO
cathieO committed Nov 8, 2019
1 parent 8a6458d commit b3765fb
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Showing 2 changed files with 47 additions and 23 deletions.
13 changes: 11 additions & 2 deletions src/GaussianFitter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -625,6 +625,11 @@ int GaussianFitter::guess_peaks(std::vector<Peak*>* results,
firstDiffs[i] = ampData[i] - ampData[i-1];
secondDiffs[i] = firstDiffs[i] - firstDiffs[i-1];
}
// for the most part any time we get to a flat portion
// we will be counting that as a peak.
// The exception is when the data never has a real peak.
// We need to ignore those waveforms
int realPeaks = 0;
for(int i = 2; i<(int)ampData.size(); i++){
if(grad == 0){
if(firstDiffs[i] > 0){
Expand All @@ -647,6 +652,9 @@ int GaussianFitter::guess_peaks(std::vector<Peak*>* results,
}else if(firstDiffs[i] < 0 ){
// flat to negative (record peak)
if(ampData[i]>noise_level){
if(prev_grad == 1){
realPeaks++;
}
//handle flat peaks
int j = i-2;
for( ; ampData[j] == ampData[i-1] ; j--);
Expand All @@ -670,6 +678,7 @@ int GaussianFitter::guess_peaks(std::vector<Peak*>* results,
}else if(firstDiffs[i] < 0){
// positive to negative (record peak)
if(ampData[i]>noise_level){
realPeaks++;
//record the peak
peak_guesses_loc.push_back(float(i-1));
peak_guesses_amp.push_back(ampData[i-1]);
Expand Down Expand Up @@ -729,11 +738,11 @@ int GaussianFitter::guess_peaks(std::vector<Peak*>* results,
//Figure out how many peaks there are
size_t peakCount = peak_guesses_loc.size();


// make a guess for the fwhm value
float neg4ln2 = -4.*log(2);
int j;
int peaks_found=0;
if(realPeaks > 0){
for(int i=0; i< peakCount; i++){
// Create a better guess by using a better width
float guess_lo = -1; // "guess" represents our guess of the width value.
Expand Down Expand Up @@ -803,7 +812,7 @@ int GaussianFitter::guess_peaks(std::vector<Peak*>* results,
peak->location = peak_guesses_loc[i];
peak->fwhm = guess;
results->push_back(peak);
}
}}
if (results->size() != 0){
results->back()->is_final_peak=true;
}
Expand Down
57 changes: 36 additions & 21 deletions src/GaussianFitter_unittests.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1042,18 +1042,23 @@ TEST_F(GaussianFitterTest, NayaniClipped1_find){
std::vector<Peak*> peaks;
int count = fitter.find_peaks(&peaks,ampData,idxData, 200);

EXPECT_EQ(2,peaks.size());
ASSERT_EQ(3,peaks.size());
EXPECT_EQ(200,peaks.at(0)->amp);
EXPECT_EQ(34 ,peaks.at(1)->amp);
EXPECT_NEAR(18.5, peaks.at(0)-> location,0.25);
EXPECT_EQ(38, peaks.at(1)->location);
EXPECT_NEAR(18.5, peaks.at(0)->location, .25);
EXPECT_NEAR(10.5, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(6, peaks.at(1)->fwhm, 1);

EXPECT_EQ(2, count);
EXPECT_EQ(43 ,peaks.at(1)->amp);
EXPECT_NEAR(30.5, peaks.at(1)->location,.25);
EXPECT_NEAR(4, peaks.at(1)->fwhm, 1);

EXPECT_EQ(34 ,peaks.at(2)->amp);
EXPECT_EQ(38, peaks.at(2)->location);
EXPECT_NEAR(6, peaks.at(2)->fwhm, 1);

EXPECT_EQ(3, count);
}

TEST_F(GaussianFitterTest, NayaniClippedi2_find){
TEST_F(GaussianFitterTest, NayaniClipped2_find){

std::vector<int> idxData;
std::vector<int> ampData;
Expand All @@ -1070,12 +1075,16 @@ TEST_F(GaussianFitterTest, NayaniClippedi2_find){
fitter.smoothing_expt(&ampData);
int count = fitter.find_peaks(&peaks,ampData,idxData, 200);

EXPECT_EQ(1,peaks.size());
ASSERT_EQ(2,peaks.size());
EXPECT_EQ(235,peaks.at(0)->amp);
EXPECT_NEAR(17.5, peaks.at(0)->location,.25);
EXPECT_NEAR(7.8, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(17.5, peaks.at(0)->location,1);
EXPECT_NEAR(7.8, peaks.at(0)->fwhm, 1);

EXPECT_EQ(29, peaks.at(1)->location);
EXPECT_EQ(15,peaks.at(1)->amp);
EXPECT_NEAR(14, peaks.at(1)->fwhm, 1);

EXPECT_EQ(1, count);
EXPECT_EQ(2, count);
}

TEST_F(GaussianFitterTest, gaussianFitter_find){
Expand Down Expand Up @@ -1152,12 +1161,15 @@ TEST_F(GaussianFitterTest, NayaniClipped4_find){
fitter.smoothing_expt(&ampData);
int count = fitter.find_peaks(&peaks,ampData,idxData, 200);

EXPECT_EQ(1,peaks.size());
ASSERT_EQ(2,peaks.size());
EXPECT_EQ(240,peaks.at(0)->amp);
EXPECT_EQ(20, peaks.at(0)->location);
EXPECT_NEAR(7.4, peaks.at(0)->fwhm, 1);

EXPECT_EQ(1, count);

EXPECT_EQ(16,peaks.at(1)->amp);
EXPECT_NEAR(29.5, peaks.at(1)->location,.25);
EXPECT_NEAR(8, peaks.at(1)->fwhm, 1);
EXPECT_EQ(2, count);
}

TEST_F(GaussianFitterTest, NayaniClipped5_find){
Expand Down Expand Up @@ -1217,14 +1229,13 @@ TEST_F(GaussianFitterTest, NayaniClipped6_find){
EXPECT_NEAR(24.5, peaks.at(1)->location,.25);
EXPECT_EQ(31, peaks.at(2)->location);
EXPECT_EQ(42, peaks.at(3)->location);
EXPECT_NEAR(6, peaks.at(0)->fwhm, 1.2);
EXPECT_NEAR(5, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(5.6, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(7.6, peaks.at(1)->fwhm, 1.25);
EXPECT_NEAR(6.6, peaks.at(2)->fwhm, 1);
EXPECT_NEAR(15, peaks.at(3)->fwhm, 1.5);
EXPECT_NEAR(16, peaks.at(3)->fwhm, 2);

EXPECT_EQ(4, count);

}

TEST_F(GaussianFitterTest, NayaniClipped7_find){
Expand All @@ -1246,15 +1257,19 @@ TEST_F(GaussianFitterTest, NayaniClipped7_find){
fitter.smoothing_expt(&ampData);
int count = fitter.find_peaks(&peaks,ampData,idxData, 200);

ASSERT_EQ(2,peaks.size());
ASSERT_EQ(3,peaks.size());
EXPECT_EQ(98,peaks.at(0)->amp);
EXPECT_EQ(168,peaks.at(1)->amp);
EXPECT_EQ(18, peaks.at(0)->location);
EXPECT_EQ(31, peaks.at(1)->location);
EXPECT_NEAR(5.2, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(10, peaks.at(1)->fwhm, 1);

EXPECT_EQ(2, count);

EXPECT_EQ(13,peaks.at(2)->amp);
EXPECT_NEAR(40.5, peaks.at(2)->location,.25);
EXPECT_NEAR(11, peaks.at(2)->fwhm, 2);

EXPECT_EQ(3, count);
}

TEST_F(GaussianFitterTest, NayaniClipped8_find){
Expand Down Expand Up @@ -1283,7 +1298,7 @@ TEST_F(GaussianFitterTest, NayaniClipped8_find){
EXPECT_NEAR(15.5,peaks.at(0)->location,0.25);
EXPECT_EQ(28,peaks.at(1)->location);
EXPECT_EQ(38,peaks.at(2)->location);
EXPECT_NEAR(9,peaks.at(0)->fwhm, 1);
EXPECT_NEAR(7,peaks.at(0)->fwhm, 1);
EXPECT_NEAR(10.8,peaks.at(1)->fwhm, 1);
EXPECT_NEAR(10.2,peaks.at(2)->fwhm, 1);

Expand Down

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