# Imaging-photoplethysmogram-extraction-pulse-rate-estimation
Tools for imaging photoplythysmogram extraction and processing
![example of imaging photoplethysmogram with corresponding EEG signal](img/EEGandIPPG.png?raw=true "Examplary imaging photoplethysmogram with corresponding EEG signal")
## Intro
Imaging photoplethysmogram (iPPG) is a technique for remote non-contact pulse rate measurement. iPPG is usually acquired from facial or palm video.
This package provides tools for iPPG signal extraction and processing. The rhesus monkeys iPPG data from [1] are used as a test dataset.
**INPUT:** video file.
**OUTPUT:** iPPG signal; estimated pulse rate.
## Content
1. extract_color_channels_from_video extracts colour signal from the video. Colour signals are computed as values of red, green and blue colour component averaged over Region of Interest (ROI) for each video frame. ROI can be selected either manually for the first frame (if only limited amount of motion is expected) or set automatically using the Viola-Jones algorithm (for iPPG extraction from human face only!). This function optionally excludes from ROI non-skin and corrupted pixels.
2. compute_ippg implements iPPG extraction methods considered in [2] (including the recently introduced CHROM and POS methods) as well as some iPPG pre- and post-processing techniques.
3. ippg_extraction_example- basic (minimal) example of using the package for estimation of pulse rate from the iPPG extracted from a video.
4. dataset_analysis - extended example of using the package for the data from [1].
5. Signal processing techniques implemented as separate m-files: wavelet_filter, wavelet_init_scales, smoothness_priors_detrending, std_sliding_win.
6. Functions for pulse rate estimation from iPPG signal:
6.1. DFT_pulse_rate_estimate uses Discrete Fourier Transform to compute average pulse rate.
6.2. wavelet_pulse_rate_estimate uses Continuous Wavelet Transform to estimate pulse rate.
7. Useful functions for comparing iPPG-based pulse rate with the ground truth:
7.1. bland_altman_plot - draws Bland Alman plot for the data.
7.2. compute_SNR - computes Signal-to-Noise Ratio (SNR) of the iPPG signal given the true pulse rate.
7.3. assess_estimation_performance - computes a number of estimation quality metrics, including root-mean-square error, mean absolute error, Pearson correlation, etc.
8. Dataset folder contains the dataset used for testing the package. The dataset was recorded from rhesus monkeys, therefore pulse rate is higher than for humans (100-250 BPM), please refer to [1] for details.
9. dataset_description.docx contains a brief description of the dataset.
Additional functionality will be added later.
## Acknowledgements
I would like to thank Gasper Slapničar for extensive testing and improving the code.
I would like to thank Dr. Cardoso for posting [the jadeR.m script](http://www.mikexcohen.com/lecturelets/eigen/jader.m), which I use to implement ICA-based iPPG extraction.
## References
[1] [Unakafov AM, Moeller S, Kagan I, Gail A, Treue S, Wolf F. Using imaging photoplethysmography for heart rate estimation in non-human primates. PLoS ONE 2018;13(8): e0202581.](https://doi.org/10.1371/journal.pone.0202581)
[2] [Unakafov AM. Pulse rate estimation using imaging photoplethysmography: generic framework and comparison of methods on a publicly available dataset. Biomedical Physics & Engineering Express. 2018;4(4):045001.](https://doi.org/10.1088%2F2057-1976%2Faabd09)
## Cite As
Unakafov AM. Imaging photoplethysmogram extraction&pulse rate estimation https://www.mathworks.com/matlabcentral/fileexchange/67527, MATLAB Central File Exchange (2018). Retrieved December 12, 2018.
Unakafov AM. Pulse rate estimation using imaging photoplethysmography: generic framework and comparison of methods on a publicly available dataset. Biomedical Physics & Engineering Express. 2018;4(4):045001. https://doi.org/10.1088%2F2057-1976%2Faabd09
Unakafov AM, Moeller S, Kagan I, Gail A, Treue S, Wolf F. Using imaging photoplethysmography for heart rate estimation in non-human primates. PLoS ONE 2018;13(8): e0202581. https://doi.org/10.1371/journal.pone.0202581
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用于成像光脉搏波提取和处理 的工具_MATLAB_代码_下载
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成像-光体积描记图-提取-脉率-估计 用于成像光脉搏波提取和处理的工具 介绍 成像光电容积描记图 (iPPG) 是一种远程非接触式脉搏率测量技术。iPPG 通常是从面部或手掌视频中获取的。该软件包提供了用于 iPPG 信号提取和处理的工具。[1] 中的恒河猴 iPPG 数据用作测试数据集。 输入:视频文件。 输出: iPPG 信号;估计的脉搏率。 内容 extract_color_channels_from_video 从视频中提取颜色信号。颜色信号被计算为在每个视频帧的感兴趣区域 (ROI) 上平均的红色、绿色和蓝色分量的值。可以为第一帧手动选择 ROI(如果预计只有有限的运动量)或使用 Viola-Jones 算法自动设置(仅用于从人脸中提取 iPPG!)。此功能可选地从 ROI 中排除非皮肤和损坏的像素。 compute_ippg 实现了 [2] 中考虑的 iPPG 提取方法(包括最近引入的 CHROM 和 POS 方法)以及一些 iPPG 预处理和后处理技术。 ippg_extraction_example-基本(最小)示例,使用该软件包从从视频中提取的 iPPG
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Imaging-photoplet-rate-estimation-master (1).zip (71个子文件)
Imaging-photoplette-estimation-master
jadeR.m 19KB
wavelet_filter.m 3KB
std_sliding_win.m 1KB
ippg_extraction_example.m 7KB
img
EEGandIPPG.png 167KB
wavelet_init_scales.m 976B
bland_altman_plot.m 3KB
assess_estimation_performance.m 2KB
smoothness_priors_detrending.m 2KB
wavelet_pulse_rate_estimate.m 3KB
LICENSE 16KB
dataset_description.docx 15KB
dataset
Session2
Session2_interframeDif.txt 97KB
Session2_ROIdata.txt 108B
Session2.bin 106KB
Session2_REF.csv 144B
Session1
Session1Region4_ROIdata.txt 109B
Session1Region2.bin 148KB
Session1Region4.bin 148KB
Session1Region1_ROIdata.txt 109B
Session1_REF.csv 192B
Session1Region5.bin 148KB
Session1Region2_ROIdata.txt 109B
Session1.bin 148KB
Session1Region1.bin 148KB
Session1_interframeDif.txt 136KB
Session1_ROIdata.txt 109B
Session1Region6.bin 148KB
Session1Region5_ROIdata.txt 109B
Session1Region6_ROIdata.txt 109B
Session10IR
Session10IR.bin 108KB
Session10IR_ROIdata.txt 108B
Session10IR_REF.csv 144B
Session2IR
Session2IR_REF.csv 144B
Session2IR.bin 106KB
Session2IR_ROIdata.txt 107B
Session3
Session3_ROIdata.txt 108B
Session3_REF.csv 224B
Session3_interframeDif.txt 148KB
Session3.bin 161KB
Session6
Session6_REF.csv 80B
Session6.bin 55KB
Session6_ROIdata.txt 108B
Session6_interframeDif.txt 50KB
Session8
Session8_CONTACT_PPG.csv 2.26MB
Session8_ROIdata.txt 108B
Session8_REF.csv 112B
Session8_interframeDif.txt 74KB
Session8.bin 82KB
Session9IR
Session9IR.bin 156KB
Session9IR_REF.csv 112B
Session9IR_ROIdata.txt 108B
Session5
Session5_REF.csv 164B
Session5.bin 120KB
Session5_ROIdata.txt 108B
Session5_interframeDif.txt 110KB
Session4
Session4_ROIdata.txt 108B
Session4_REF.csv 128B
Session4_interframeDif.txt 173KB
Session4.bin 188KB
Session7
Session7.bin 293KB
Session7_REF.csv 404B
Session7_ROIdata.txt 110B
Session7_interframeDif.txt 268KB
summary.txt 374B
DFT_pulse_rate_estimate.m 2KB
compute_ippg.m 11KB
compute_SNR.m 2KB
dataset_analysis.m 15KB
README.md 4KB
extract_color_channels_from_video.m 9KB
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