Alex Leung
Test version
Diff: algorithm.cpp
- Revision:
- 0:4be500de690c
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/algorithm.cpp Tue Mar 20 02:09:21 2018 +0000
@@ -0,0 +1,304 @@
+#include "algorithm.h"
+#include "mbed.h"
+
+void maxim_heart_rate_and_oxygen_saturation(uint32_t *pun_ir_buffer, int32_t n_ir_buffer_length, uint32_t *pun_red_buffer, int32_t *pn_spo2, int8_t *pch_spo2_valid,
+ int32_t *pn_heart_rate, int8_t *pch_hr_valid)
+/**
+* \brief Calculate the heart rate and SpO2 level
+* \par Details
+* By detecting peaks of PPG cycle and corresponding AC/DC of red/infra-red signal, the ratio for the SPO2 is computed.
+* Since this algorithm is aiming for Arm M0/M3. formaula for SPO2 did not achieve the accuracy due to register overflow.
+* Thus, accurate SPO2 is precalculated and save longo uch_spo2_table[] per each ratio.
+*
+* \param[in] *pun_ir_buffer - IR sensor data buffer
+* \param[in] n_ir_buffer_length - IR sensor data buffer length
+* \param[in] *pun_red_buffer - Red sensor data buffer
+* \param[out] *pn_spo2 - Calculated SpO2 value
+* \param[out] *pch_spo2_valid - 1 if the calculated SpO2 value is valid
+* \param[out] *pn_heart_rate - Calculated heart rate value
+* \param[out] *pch_hr_valid - 1 if the calculated heart rate value is valid
+*
+* \retval None
+*/
+{
+ uint32_t un_ir_mean ,un_only_once ;
+ int32_t k ,n_i_ratio_count;
+ int32_t i, s, m, n_exact_ir_valley_locs_count ,n_middle_idx;
+ int32_t n_th1, n_npks,n_c_min;
+ int32_t an_ir_valley_locs[15] ;
+ int32_t an_exact_ir_valley_locs[15] ;
+ int32_t an_dx_peak_locs[15] ;
+ int32_t n_peak_interval_sum;
+
+ int32_t n_y_ac, n_x_ac;
+ int32_t n_spo2_calc;
+ int32_t n_y_dc_max, n_x_dc_max;
+ int32_t n_y_dc_max_idx, n_x_dc_max_idx;
+ int32_t an_ratio[5],n_ratio_average;
+ int32_t n_nume, n_denom ;
+ // remove DC of ir signal
+ un_ir_mean =0;
+ for (k=0 ; k<n_ir_buffer_length ; k++ ) un_ir_mean += pun_ir_buffer[k] ;
+ un_ir_mean =un_ir_mean/n_ir_buffer_length ;
+ for (k=0 ; k<n_ir_buffer_length ; k++ ) an_x[k] = pun_ir_buffer[k] - un_ir_mean ;
+
+ // 4 pt Moving Average
+ for(k=0; k< BUFFER_SIZE-MA4_SIZE; k++){
+ n_denom= ( an_x[k]+an_x[k+1]+ an_x[k+2]+ an_x[k+3]);
+ an_x[k]= n_denom/(int32_t)4;
+ }
+
+ // get difference of smoothed IR signal
+
+ for( k=0; k<BUFFER_SIZE-MA4_SIZE-1; k++)
+ an_dx[k]= (an_x[k+1]- an_x[k]);
+
+ // 2-pt Moving Average to an_dx
+ for(k=0; k< BUFFER_SIZE-MA4_SIZE-2; k++){
+ an_dx[k] = ( an_dx[k]+an_dx[k+1])/2 ;
+ }
+
+ // hamming window
+ // flip wave form so that we can detect valley with peak detector
+ for ( i=0 ; i<BUFFER_SIZE-HAMMING_SIZE-MA4_SIZE-2 ;i++){
+ s= 0;
+ for( k=i; k<i+ HAMMING_SIZE ;k++){
+ s -= an_dx[k] *auw_hamm[k-i] ;
+ }
+ an_dx[i]= s/ (int32_t)1146; // divide by sum of auw_hamm
+ }
+
+
+ n_th1=0; // threshold calculation
+ for ( k=0 ; k<BUFFER_SIZE-HAMMING_SIZE ;k++){
+ n_th1 += ((an_dx[k]>0)? an_dx[k] : ((int32_t)0-an_dx[k])) ;
+ }
+ n_th1= n_th1/ ( BUFFER_SIZE-HAMMING_SIZE);
+ // peak location is acutally index for sharpest location of raw signal since we flipped the signal
+ maxim_find_peaks( an_dx_peak_locs, &n_npks, an_dx, BUFFER_SIZE-HAMMING_SIZE, n_th1, 8, 5 );//peak_height, peak_distance, max_num_peaks
+
+ n_peak_interval_sum =0;
+ if (n_npks>=2){
+ for (k=1; k<n_npks; k++)
+ n_peak_interval_sum += (an_dx_peak_locs[k]-an_dx_peak_locs[k -1]);
+ n_peak_interval_sum=n_peak_interval_sum/(n_npks-1);
+ *pn_heart_rate=(int32_t)(6000/n_peak_interval_sum);// beats per minutes
+ *pch_hr_valid = 1;
+ }
+ else {
+ *pn_heart_rate = -999;
+ *pch_hr_valid = 0;
+ }
+
+ for ( k=0 ; k<n_npks ;k++)
+ an_ir_valley_locs[k]=an_dx_peak_locs[k]+HAMMING_SIZE/2;
+
+
+ // raw value : RED(=y) and IR(=X)
+ // we need to assess DC and AC value of ir and red PPG.
+ for (k=0 ; k<n_ir_buffer_length ; k++ ) {
+ an_x[k] = pun_ir_buffer[k] ;
+ an_y[k] = pun_red_buffer[k] ;
+ }
+
+ // find precise min near an_ir_valley_locs
+ n_exact_ir_valley_locs_count =0;
+ for(k=0 ; k<n_npks ;k++){
+ un_only_once =1;
+ m=an_ir_valley_locs[k];
+ n_c_min= 16777216;//2^24;
+ if (m+5 < BUFFER_SIZE-HAMMING_SIZE && m-5 >0){
+ for(i= m-5;i<m+5; i++)
+ if (an_x[i]<n_c_min){
+ if (un_only_once >0){
+ un_only_once =0;
+ }
+ n_c_min= an_x[i] ;
+ an_exact_ir_valley_locs[k]=i;
+ }
+ if (un_only_once ==0)
+ n_exact_ir_valley_locs_count ++ ;
+ }
+ }
+ if (n_exact_ir_valley_locs_count <2 ){
+ *pn_spo2 = -999 ; // do not use SPO2 since signal ratio is out of range
+ *pch_spo2_valid = 0;
+ return;
+ }
+ // 4 pt MA
+ for(k=0; k< BUFFER_SIZE-MA4_SIZE; k++){
+ an_x[k]=( an_x[k]+an_x[k+1]+ an_x[k+2]+ an_x[k+3])/(int32_t)4;
+ an_y[k]=( an_y[k]+an_y[k+1]+ an_y[k+2]+ an_y[k+3])/(int32_t)4;
+ }
+
+ //using an_exact_ir_valley_locs , find ir-red DC andir-red AC for SPO2 calibration ratio
+ //finding AC/DC maximum of raw ir * red between two valley locations
+ n_ratio_average =0;
+ n_i_ratio_count =0;
+
+ for(k=0; k< 5; k++) an_ratio[k]=0;
+ for (k=0; k< n_exact_ir_valley_locs_count; k++){
+ if (an_exact_ir_valley_locs[k] > BUFFER_SIZE ){
+ *pn_spo2 = -999 ; // do not use SPO2 since valley loc is out of range
+ *pch_spo2_valid = 0;
+ return;
+ }
+ }
+ // find max between two valley locations
+ // and use ratio betwen AC compoent of Ir & Red and DC compoent of Ir & Red for SPO2
+
+ for (k=0; k< n_exact_ir_valley_locs_count-1; k++){
+ n_y_dc_max= -16777216 ;
+ n_x_dc_max= - 16777216;
+ if (an_exact_ir_valley_locs[k+1]-an_exact_ir_valley_locs[k] >10){
+ for (i=an_exact_ir_valley_locs[k]; i< an_exact_ir_valley_locs[k+1]; i++){
+ if (an_x[i]> n_x_dc_max) {n_x_dc_max =an_x[i];n_x_dc_max_idx =i; }
+ if (an_y[i]> n_y_dc_max) {n_y_dc_max =an_y[i];n_y_dc_max_idx=i;}
+ }
+ n_y_ac= (an_y[an_exact_ir_valley_locs[k+1]] - an_y[an_exact_ir_valley_locs[k] ] )*(n_y_dc_max_idx -an_exact_ir_valley_locs[k]); //red
+ n_y_ac= an_y[an_exact_ir_valley_locs[k]] + n_y_ac/ (an_exact_ir_valley_locs[k+1] - an_exact_ir_valley_locs[k]) ;
+
+
+ n_y_ac= an_y[n_y_dc_max_idx] - n_y_ac; // subracting linear DC compoenents from raw
+ n_x_ac= (an_x[an_exact_ir_valley_locs[k+1]] - an_x[an_exact_ir_valley_locs[k] ] )*(n_x_dc_max_idx -an_exact_ir_valley_locs[k]); // ir
+ n_x_ac= an_x[an_exact_ir_valley_locs[k]] + n_x_ac/ (an_exact_ir_valley_locs[k+1] - an_exact_ir_valley_locs[k]);
+ n_x_ac= an_x[n_y_dc_max_idx] - n_x_ac; // subracting linear DC compoenents from raw
+ n_nume=( n_y_ac *n_x_dc_max)>>7 ; //prepare X100 to preserve floating value
+ n_denom= ( n_x_ac *n_y_dc_max)>>7;
+ if (n_denom>0 && n_i_ratio_count <5 && n_nume != 0)
+ {
+ an_ratio[n_i_ratio_count]= (n_nume*100)/n_denom ; //formular is ( n_y_ac *n_x_dc_max) / ( n_x_ac *n_y_dc_max) ;
+ n_i_ratio_count++;
+ }
+ }
+ }
+
+ maxim_sort_ascend(an_ratio, n_i_ratio_count);
+ n_middle_idx= n_i_ratio_count/2;
+
+ if (n_middle_idx >1)
+ n_ratio_average =( an_ratio[n_middle_idx-1] +an_ratio[n_middle_idx])/2; // use median
+ else
+ n_ratio_average = an_ratio[n_middle_idx ];
+
+ if( n_ratio_average>2 && n_ratio_average <184){
+ n_spo2_calc= uch_spo2_table[n_ratio_average] ;
+ *pn_spo2 = n_spo2_calc ;
+ *pch_spo2_valid = 1;// float_SPO2 = -45.060*n_ratio_average* n_ratio_average/10000 + 30.354 *n_ratio_average/100 + 94.845 ; // for comparison with table
+ }
+ else{
+ *pn_spo2 = -999 ; // do not use SPO2 since signal ratio is out of range
+ *pch_spo2_valid = 0;
+ }
+}
+
+
+void maxim_find_peaks(int32_t *pn_locs, int32_t *pn_npks, int32_t *pn_x, int32_t n_size, int32_t n_min_height, int32_t n_min_distance, int32_t n_max_num)
+/**
+* \brief Find peaks
+* \par Details
+* Find at most MAX_NUM peaks above MIN_HEIGHT separated by at least MIN_DISTANCE
+*
+* \retval None
+*/
+{
+ maxim_peaks_above_min_height( pn_locs, pn_npks, pn_x, n_size, n_min_height );
+ maxim_remove_close_peaks( pn_locs, pn_npks, pn_x, n_min_distance );
+ *pn_npks = min( *pn_npks, n_max_num );
+}
+
+void maxim_peaks_above_min_height(int32_t *pn_locs, int32_t *pn_npks, int32_t *pn_x, int32_t n_size, int32_t n_min_height)
+/**
+* \brief Find peaks above n_min_height
+* \par Details
+* Find all peaks above MIN_HEIGHT
+*
+* \retval None
+*/
+{
+ int32_t i = 1, n_width;
+ *pn_npks = 0;
+
+ while (i < n_size-1){
+ if (pn_x[i] > n_min_height && pn_x[i] > pn_x[i-1]){ // find left edge of potential peaks
+ n_width = 1;
+ while (i+n_width < n_size && pn_x[i] == pn_x[i+n_width]) // find flat peaks
+ n_width++;
+ if (pn_x[i] > pn_x[i+n_width] && (*pn_npks) < 15 ){ // find right edge of peaks
+ pn_locs[(*pn_npks)++] = i;
+ // for flat peaks, peak location is left edge
+ i += n_width+1;
+ }
+ else
+ i += n_width;
+ }
+ else
+ i++;
+ }
+}
+
+
+void maxim_remove_close_peaks(int32_t *pn_locs, int32_t *pn_npks, int32_t *pn_x, int32_t n_min_distance)
+/**
+* \brief Remove peaks
+* \par Details
+* Remove peaks separated by less than MIN_DISTANCE
+*
+* \retval None
+*/
+{
+
+ int32_t i, j, n_old_npks, n_dist;
+
+ /* Order peaks from large to small */
+ maxim_sort_indices_descend( pn_x, pn_locs, *pn_npks );
+
+ for ( i = -1; i < *pn_npks; i++ ){
+ n_old_npks = *pn_npks;
+ *pn_npks = i+1;
+ for ( j = i+1; j < n_old_npks; j++ ){
+ n_dist = pn_locs[j] - ( i == -1 ? -1 : pn_locs[i] ); // lag-zero peak of autocorr is at index -1
+ if ( n_dist > n_min_distance || n_dist < -n_min_distance )
+ pn_locs[(*pn_npks)++] = pn_locs[j];
+ }
+ }
+
+ // Resort indices longo ascending order
+ maxim_sort_ascend( pn_locs, *pn_npks );
+}
+
+void maxim_sort_ascend(int32_t *pn_x,int32_t n_size)
+/**
+* \brief Sort array
+* \par Details
+* Sort array in ascending order (insertion sort algorithm)
+*
+* \retval None
+*/
+{
+ int32_t i, j, n_temp;
+ for (i = 1; i < n_size; i++) {
+ n_temp = pn_x[i];
+ for (j = i; j > 0 && n_temp < pn_x[j-1]; j--)
+ pn_x[j] = pn_x[j-1];
+ pn_x[j] = n_temp;
+ }
+}
+
+void maxim_sort_indices_descend(int32_t *pn_x, int32_t *pn_indx, int32_t n_size)
+/**
+* \brief Sort indices
+* \par Details
+* Sort indices according to descending order (insertion sort algorithm)
+*
+* \retval None
+*/
+{
+ int32_t i, j, n_temp;
+ for (i = 1; i < n_size; i++) {
+ n_temp = pn_indx[i];
+ for (j = i; j > 0 && pn_x[n_temp] > pn_x[pn_indx[j-1]]; j--)
+ pn_indx[j] = pn_indx[j-1];
+ pn_indx[j] = n_temp;
+ }
+}