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feat: add findPeaks Function

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This commit is contained in:
kradchen
2025-10-23 15:49:32 +08:00
parent 52da7bcd35
commit 6b16f6e01a
6 changed files with 240 additions and 4 deletions
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84
src/Function2D.cpp
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@@ -1034,3 +1034,87 @@ Matrix Aurora::sub2ind(const Matrix &aVMatrixSize, std::initializer_list<Matrix>
delete [] strides;
return Matrix::New(output,returnVectorSize,1,1);
}
void Aurora::findPeaksHost(const Matrix & aData, int aNPeaks, float aMinPeakHeight, float MinPeakProminece,
int* outIndex)
{
int signalSize = aData.getDimSize(0);
int signalCount = aData.getDimSize(1);
#pragma omp parallel for
for (size_t threadIndex = 0; threadIndex < signalCount; threadIndex++)
{
float* dataPointer = aData.getData() + threadIndex*signalSize ;
float newPeak = dataPointer[0];
float newValley = dataPointer[0];
int peakIndex = 0;
float higherValley;
int indexs[32];
float values[32];
for (size_t i = 0; i < aNPeaks; i++)
{
indexs[i] = signalSize;
values[i] = 0;
}
int save_index=0;
for (int i = 1; i < signalSize - 1; ++i)
{
// find peaks
if (dataPointer[i] > dataPointer[i - 1] && dataPointer[i] > dataPointer[i + 1])
{
newPeak = dataPointer[i];
peakIndex = i;
};
// find valley
if (dataPointer[i] < dataPointer[i - 1] && dataPointer[i] < dataPointer[i + 1])
{
higherValley = std::max(newValley, dataPointer[i]);
newValley = dataPointer[i];
if (newPeak >= aMinPeakHeight)
{
float prominece = newPeak - higherValley;
if (prominece >= MinPeakProminece)
{
if (save_index < aNPeaks)
{
values[save_index] = newPeak;
indexs[save_index] = peakIndex;
save_index++;
}
else
{
for (size_t j = 0; j < aNPeaks; j++)
{
if (values[j] < newPeak)
{
std::swap(values[j], newPeak);
std::swap(indexs[j], peakIndex);
}
}
}
}
}
}
}
if (save_index>=aNPeaks)
{
for (size_t i = 0; i < aNPeaks; i++)
{
for (size_t j = i+1; j < aNPeaks; j++)
{
if (indexs[i]>indexs[j])
{
std::swap(values[j], values[i]);
std::swap(indexs[j], indexs[i]);
}
}
}
}
for (size_t i = 0; i < aNPeaks; i++)
{
// aOutPeaks[threadIndex*aNPeaks+i] = values[i];
outIndex[threadIndex*aNPeaks+i] = indexs[i];
}
}
}

106
src/Function2D.cu
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@@ -1711,7 +1711,7 @@ __global__ void validKernel(const float* aData, const float* aValid, float* aOut
}
}
Aurora::CudaMatrix Aurora::valid(const Aurora::CudaMatrix aData, const Aurora::CudaMatrix aValid)
Aurora::CudaMatrix Aurora::valid(const Aurora::CudaMatrix& aData, const Aurora::CudaMatrix aValid)
{
auto validEnable = Aurora::sum(aValid);
if(validEnable.toHostMatrix()[0] == 0)
@@ -1748,3 +1748,107 @@ Aurora::CudaMatrix Aurora::valid(const Aurora::CudaMatrix aData, const Aurora::C
delete[] validProcessed;
return Aurora::CudaMatrix::fromRawData(result, rowCount, validColumnCount);
}
__global__ void findPeaksKernel(float* aData, int aSignalSize, int aSignalCount, int aNPeaks, float aMinPeakHeight, float MinPeakProminece,
float* aOutPeaks, int* outIndex)
{
int threadIndex = blockIdx.x * blockDim.x;
float* dataPointer = aData + threadIndex*aSignalSize ;
float newPeak = dataPointer[0];
float newValley = dataPointer[0];
float higherValley;
__shared__ int indexs[32];
__shared__ float values[32];
for (size_t i = 0; i < aNPeaks; i++)
{
indexs[i] = aSignalSize;
values[i] = 0;
}
int save_index = 0;
int peakIndex = -1;
{
for(int i=1; i < aSignalSize-1; ++i)
{
//find peaks
if (dataPointer[i]>dataPointer[i-1] && dataPointer[i]>dataPointer[i+1]){
newPeak= dataPointer[i];
peakIndex = i;
};
//find valley
if (dataPointer[i]<dataPointer[i-1] && dataPointer[i]<dataPointer[i+1]){
higherValley = max(newValley,dataPointer[i]);
newValley = dataPointer[i];
if (newPeak>=aMinPeakHeight)
{
float prominece = newPeak-higherValley;
if (prominece>=MinPeakProminece)
{
if (save_index < aNPeaks){
values[save_index] = newPeak;
indexs[save_index] = peakIndex;
save_index ++;
}
else{
float tempPeak = newPeak;
int tempIndex = peakIndex;
for (size_t j = 0; j < aNPeaks; j++)
{
if (values[j]<newPeak)
{
tempPeak = values[j];
tempIndex = indexs[j];
values[j] = newPeak;
indexs[j] = peakIndex;
newPeak = tempPeak;
peakIndex = tempIndex;
}
}
}
}
}
};
}
}
if (save_index>=aNPeaks)
{
for (size_t i = 0; i < aNPeaks; i++)
{
for (size_t j = i+1; j < aNPeaks; j++)
{
if (indexs[i]>indexs[j])
{
int temp = indexs[j];
indexs[j] = indexs[i];
indexs[i] = temp;
float tempValue = values[j];
values[j] = values[i];
values[i] = tempValue;
}
}
}
}
for (size_t i = 0; i < aNPeaks; i++)
{
aOutPeaks[threadIndex*aNPeaks+i] = values[i];
outIndex[threadIndex*aNPeaks+i] = indexs[i];
}
}
Aurora::CudaMatrix Aurora::findPeaks(const Aurora::CudaMatrix& aData, int aNpeaks, float aMinPeakHeight, float aMinPeakProminence,int** aOutIndexs )
{
int rowCount = aData.getDimSize(0);
int colCount = aData.getDimSize(1);
float* peaks = nullptr ;
cudaMalloc((void**)&peaks, sizeof(float) * aNpeaks * colCount );
cudaMalloc((void**)aOutIndexs, sizeof(int) * aNpeaks * colCount );
int threadPerBlock = 256;
int blockPerGrid = colCount / threadPerBlock + 1;
findPeaksKernel<<<colCount, 1>>>(aData.getData(), rowCount, colCount, aNpeaks, aMinPeakHeight, aMinPeakProminence,peaks,*aOutIndexs);
cudaDeviceSynchronize();
// cudaFree(peaks);
return Aurora::CudaMatrix::fromRawData(peaks, aNpeaks, colCount);
}

13
src/Function2D.cuh
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@@ -87,8 +87,19 @@ namespace Aurora
*/
CudaMatrix ifft_symmetric(const CudaMatrix &aMatrix,long aLength);
CudaMatrix valid(const CudaMatrix aData, const CudaMatrix aValid);
CudaMatrix valid(const CudaMatrix& aData, const CudaMatrix aValid);
/**
* findPeaks 按列进行峰查找和匹配
* @attention 不要给aOutIndexs提前分配内存
* @param aData 输入
* @param aNpeaks 峰数量
* @param aMinPeakHeight 最小高度
* @param aMinPeakProminence 最小相对高度
* @param aOutIndexs 空指针，会在函数内分配device内存
* @return 筛选出的峰高度
*/
CudaMatrix findPeaks(const CudaMatrix& aData, int aNpeaks, float aMinPeakHeight, float aMinPeakProminence, int** aOutIndexs);
}
#endif // __FUNCTION2D_CUDA_H__

2
src/Function2D.h
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@@ -178,7 +178,7 @@ namespace Aurora
* @return
*/
Matrix sub2ind(const Matrix &aVMatrixSize, std::initializer_list<Matrix> aSliceIdxs);
void findPeaksHost(const Matrix & aData, int aNPeaks, float aMinPeakHeight, float MinPeakProminece,int* outIndex);
};
#endif // AURORA_FUNCTION2D_H

21
test/Function2D_Cuda_Test.cpp
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@@ -5,6 +5,7 @@
#include "Function.h"
#include "Matrix.h"
#include "TestUtility.h"
#include "MatlabReader.h"
#include "Function2D.h"
#include "Function2D.cuh"
@@ -18,11 +19,15 @@ protected:
static void TearDownTestCase(){
}
public:
Aurora::Matrix mSignal;
Aurora::CudaMatrix dmSignal;
Aurora::Matrix B;
Aurora::CudaMatrix dB;
void SetUp(){
MatlabReader m("/home/krad/TestData/peaks.mat");
mSignal = m.read("AScan_env_norm");
dmSignal = mSignal.toDeviceMatrix();
}
void TearDown(){
}
@@ -997,3 +1002,17 @@ TEST_F(Function2D_Cuda_Test, hilbert) {
EXPECT_NEAR(ret1[i], ret2.getValue(i), 0.01);
}
}
TEST_F(Function2D_Cuda_Test, findPeaks) {
int* indexs = new int[mSignal.getDimSize(1)*10];
auto ret1 = Aurora::findPeaks(dmSignal,10, 0.2, 0.05,indexs);
auto reH = ret1.toHostMatrix();
for(unsigned int i=0; i<10; ++i)
{
printf("%d,",indexs[i]);
}
delete [] indexs;
}

18
test/Function2D_Test.cpp
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@@ -2,6 +2,8 @@
#include <vector>
#include "TestUtility.h"
#include "MatlabReader.h"
#include "Matrix.h"
#include "Function.h"
#include "Function1D.h"
@@ -16,7 +18,11 @@ protected:
}
static void TearDownTestCase(){
}
public:
Aurora::Matrix mSignal;
void SetUp(){
MatlabReader m("/home/krad/TestData/peaks.mat");
mSignal = m.read("AScan_env_norm");
}
void TearDown(){
}
@@ -573,3 +579,15 @@ TEST_F(Function2D_Test, sub2ind) {
}
TEST_F(Function2D_Test, findPeaks) {
int* indexs = new int[mSignal.getDimSize(1)*10];
Aurora::findPeaksHost(mSignal,10, 0.2, 0.05,indexs);
for(unsigned int i=0; i<10; ++i)
{
printf("%d,",indexs[i]);
}
delete [] indexs;
}