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modified unit tests #320 and modified gaussianSum() #355
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@FloCiaglia
FloCiaglia committed Nov 6, 2019
1 parent eeaed34 commit 3f17cf4
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Showing 2 changed files with 64 additions and 34 deletions.
26 changes: 20 additions & 6 deletions src/GaussianFitter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -91,9 +91,9 @@ double gaussianSum(const gsl_vector * x,const double t)
for(i=0;i<(x->size/3);i++){
double a = gsl_vector_get(x,3*i+0);
double b = gsl_vector_get(x,3*i+1);
double c = gsl_vector_get(x,3*i+2);
const double z = (t - b) / c;
value += (a * exp(-0.5 * z * z));
double w = gsl_vector_get(x,3*i+2);
const double z = (t - b) / w;
value += (a * exp(-4 * log(2) * z * z));
}
return value;
}
Expand Down Expand Up @@ -640,13 +640,27 @@ int GaussianFitter::guess_peaks(std::vector<Peak*>* results,
if (grad == 1){
// sloping down
if(ampData[i+1] < ampData[i]){
if(ampData[i]>=noise_level){
if(ampData[i]>noise_level){

//handle long flat peaks
// float toll = ampData[i]*.02;
float toll = 0;
int j = i-1;

for( j = i-1;
ampData[j] > ampData[i]-toll &&
ampData[j] < ampData[i] + toll;
j--);
float lenOfFlat = i -j -1;
//this is truncating, we need
//to fix this
int loc = i - lenOfFlat/2;
//record the peak
peak_guesses_loc.push_back(i);
peak_guesses_loc.push_back(loc);
}
//now we are sloping down
grad = -1;
}
}
//Peak location
// previously decreasing
}else if(grad == -1){
Expand Down
72 changes: 44 additions & 28 deletions src/GaussianFitter_unittests.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -104,8 +104,11 @@ TEST_F(GaussianFitterTest, NayaniClippedi2_guess){

EXPECT_EQ(1,peaks.size());
EXPECT_EQ(235,peaks.at(0)->amp);
EXPECT_EQ(15,peaks.at(1)->amp);
EXPECT_EQ(18, peaks.at(0)->location);
EXPECT_EQ(29, peaks.at(1)->location);
EXPECT_NEAR(7.8, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(14, peaks.at(1)->fwhm, 1);

EXPECT_EQ(1, count);
}
Expand All @@ -128,12 +131,15 @@ TEST_F(GaussianFitterTest, gaussianFitter_guess){
std::vector<Peak*> peaks;
int count = fitter.guess_peaks(&peaks, ampData, idxData);

EXPECT_EQ(1,peaks.size());
EXPECT_EQ(2,peaks.size());
EXPECT_EQ(240,peaks.at(0)->amp);
EXPECT_EQ(15,peaks.at(1)->amp);
EXPECT_EQ(17, peaks.at(0)->location);
EXPECT_EQ(28, peaks.at(1)->location);
EXPECT_NEAR(6, peaks.at(0)->fwhm,1);
EXPECT_NEAR(10.6, peaks.at(1)->fwhm,1);

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

}

Expand All @@ -155,12 +161,15 @@ TEST_F(GaussianFitterTest, NayaniClipped3_guess){
std::vector<Peak*> peaks;
int count = fitter.guess_peaks(&peaks, ampData, idxData);

EXPECT_EQ(1,peaks.size());
EXPECT_EQ(2,peaks.size());
EXPECT_EQ(238,peaks.at(0)->amp);
EXPECT_EQ(15,peaks.at(1)->amp);
EXPECT_EQ(19, peaks.at(0)->location);
EXPECT_EQ(31, peaks.at(1)->location);
EXPECT_NEAR(5.9, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(8.6, peaks.at(1)->fwhm, 1);

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


Expand Down Expand Up @@ -239,18 +248,21 @@ TEST_F(GaussianFitterTest, NayaniClipped6_guess){
std::vector<Peak*> peaks;
int count = fitter.guess_peaks(&peaks, ampData, idxData);

EXPECT_EQ(3,peaks.size());
EXPECT_EQ(193,peaks.at(0)->amp);
EXPECT_EQ(151,peaks.at(1)->amp);
EXPECT_EQ(12, peaks.at(2)->amp);
EXPECT_EQ(24, peaks.at(0)->location);
EXPECT_EQ(31, peaks.at(1)->location);
EXPECT_EQ(43, peaks.at(2)->location);
EXPECT_NEAR(7.6, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(6.6, peaks.at(1)->fwhm, 1);
EXPECT_NEAR(14, peaks.at(2)->fwhm, 1);
EXPECT_EQ(4,peaks.size());
EXPECT_EQ(11,peaks.at(0)->amp);
EXPECT_EQ(193,peaks.at(1)->amp);
EXPECT_EQ(151,peaks.at(2)->amp);
EXPECT_EQ(12, peaks.at(3)->amp);
EXPECT_EQ(13, peaks.at(0)->location);
EXPECT_EQ(25, peaks.at(1)->location);
EXPECT_EQ(31, peaks.at(2)->location);
EXPECT_EQ(43, peaks.at(3)->location);
EXPECT_NEAR(5.6, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(7.6, peaks.at(1)->fwhm, 1);
EXPECT_NEAR(6.6, peaks.at(2)->fwhm, 1);
EXPECT_NEAR(14, peaks.at(3)->fwhm, 1);

EXPECT_EQ(3, count);
EXPECT_EQ(4, count);
}

TEST_F(GaussianFitterTest, NayaniClipped7_guess){
Expand Down Expand Up @@ -369,22 +381,24 @@ TEST_F(GaussianFitterTest, max_iter_2_guess){

parseWave(input, idxData, ampData);


// now that we have the input vectors call the gaussianFitter
GaussianFitter fitter;
fitter.noise_level = 9;
std::vector<Peak*> peaks;
int count = fitter.guess_peaks(&peaks, ampData, idxData);

EXPECT_EQ(2,peaks.size());
EXPECT_EQ(3,peaks.size());
EXPECT_EQ(139,peaks.at(0)->amp);
EXPECT_EQ(26,peaks.at(1)->amp);
EXPECT_EQ(10,peaks.at(1)->amp);
EXPECT_EQ(26,peaks.at(2)->amp);
EXPECT_EQ(16, peaks.at(0)->location);
EXPECT_EQ(58, peaks.at(1)->location);
EXPECT_EQ(27, peaks.at(1)->location);
EXPECT_EQ(58, peaks.at(2)->location);
EXPECT_NEAR(5, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(4.6, peaks.at(1)->fwhm, 1);
EXPECT_NEAR(5.2, peaks.at(1)->fwhm, 1);
EXPECT_NEAR(4.6, peaks.at(2)->fwhm, 1);

EXPECT_EQ(2, count);
EXPECT_EQ(3, count);
}
//Exceeding max no of iterations
TEST_F(GaussianFitterTest, max_iter_3_guess){
Expand Down Expand Up @@ -479,7 +493,7 @@ TEST_F(GaussianFitterTest, max_iter_5_guess){
std::vector<Peak*> peaks;
int count = fitter.guess_peaks(&peaks, ampData, idxData);

ASSERT_EQ(7,peaks.size());
EXPECT_EQ(7,peaks.size());
EXPECT_EQ(88,peaks.at(0)->amp);
EXPECT_EQ(34,peaks.at(1)->amp);
EXPECT_EQ(20,peaks.at(2)->amp);
Expand Down Expand Up @@ -647,7 +661,7 @@ TEST_F(GaussianFitterTest, problem_waveform_2_guess){
EXPECT_NEAR(6.2, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(5.4, peaks.at(0)->fwhm, 1);

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

}
//3
Expand Down Expand Up @@ -754,8 +768,8 @@ TEST_F(GaussianFitterTest, problem_waveform_6_guess){
EXPECT_EQ(2,peaks.size());
EXPECT_EQ(181, peaks.at(0)->amp);
EXPECT_EQ(12, peaks.at(1)->amp);
EXPECT_EQ(19, peaks.at(0)->location);
EXPECT_EQ(19, peaks.at(1)->location);
EXPECT_EQ(18, peaks.at(0)->location);
EXPECT_EQ(30, peaks.at(1)->location);
EXPECT_NEAR(5.5, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(6, peaks.at(1)->fwhm, 1);

Expand Down Expand Up @@ -837,7 +851,7 @@ TEST_F(GaussianFitterTest, problem_waveform_9_guess){
EXPECT_EQ(19, peaks.at(0)->location);
EXPECT_EQ(29, peaks.at(1)->location);
EXPECT_NEAR(6.8, peaks.at(0)->fwhm, 1);
EXPECT_NEAR(9, peaks.at(1)->fwhm, 1);
EXPECT_NEAR(12, peaks.at(1)->fwhm, 1);

EXPECT_EQ(2, count);
}
Expand Down Expand Up @@ -1034,7 +1048,7 @@ TEST_F(GaussianFitterTest, NayaniClipped1_find){
EXPECT_EQ(2,count);
}
*/
TEST_F(GaussianFitterTest, NayaniClippedi2_find){

std::vector<int> idxData;
Expand All @@ -1047,6 +1061,7 @@ TEST_F(GaussianFitterTest, NayaniClippedi2_find){
parseWave(input, idxData, ampData);

GaussianFitter fitter;
fitter.noise_level = 9;
std::vector<Peak*> peaks;
fitter.smoothing_expt(&ampData);
int count = fitter.find_peaks(&peaks,ampData,idxData, 200);
Expand All @@ -1070,6 +1085,7 @@ TEST_F(GaussianFitterTest, gaussianFitter_find){
parseWave(input, idxData, ampData);

GaussianFitter fitter;
fitter.noise_level = 9;
std::vector<Peak*> peaks;
fitter.smoothing_expt(&ampData);
int count = fitter.find_peaks(&peaks,ampData,idxData, 200);
Expand All @@ -1085,7 +1101,7 @@ TEST_F(GaussianFitterTest, gaussianFitter_find){
EXPECT_EQ(2, count);
}

/*
TEST_F(GaussianFitterTest, NayaniClipped3_find){
// create a vector of integers
Expand Down

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