File content as of revision 5:648aa1e83d65:

/** \file algorithm.cpp ******************************************************
*
* Project: MAXREFDES117#
* Filename: algorithm.cpp
* Description: This module calculates the heart rate/SpO2 level
*
*
* --------------------------------------------------------------------
*
* This code follows the following naming conventions:
*
* char              ch_pmod_value
* char (array)      s_pmod_s_string[16]
* float             f_pmod_value
* int32_t           n_pmod_value
* int32_t (array)   an_pmod_value[16]
* int16_t           w_pmod_value
* int16_t (array)   aw_pmod_value[16]
* uint16_t          uw_pmod_value
* uint16_t (array)  auw_pmod_value[16]
* uint8_t           uch_pmod_value
* uint8_t (array)   auch_pmod_buffer[16]
* uint32_t          un_pmod_value
* int32_t *         pn_pmod_value
*
* ------------------------------------------------------------------------- */
/*******************************************************************************
* Copyright (C) 2016 Maxim Integrated Products, Inc., All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL MAXIM INTEGRATED BE LIABLE FOR ANY CLAIM, DAMAGES
* OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
* ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*
* Except as contained in this notice, the name of Maxim Integrated
* Products, Inc. shall not be used except as stated in the Maxim Integrated
* Products, Inc. Branding Policy.
*
* The mere transfer of this software does not imply any licenses
* of trade secrets, proprietary technology, copyrights, patents,
* trademarks, maskwork rights, or any other form of intellectual
* property whatsoever. Maxim Integrated Products, Inc. retains all
* ownership rights.
*******************************************************************************
*/
#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;
    }
}