Heart Rate

Second Advanced Numerical Methods Project

Getting Started

These instructions will install the development environment into your local machine.

Prerequisites

Clone the repository

$ git clone https://github.com/juanmbellini/heart_rate.git

Install Python and pip

MacOS

A. Install packages

$ brew install python

B. Update the PATH variable to use the Homebrew's python packages

$ echo 'export PATH="/usr/local/opt/python/libexec/bin:$PATH" # Use Homebrew python' >> ~/.bash_profile
$ source ~/.bash_profile

Ubuntu

$ sudo apt-get install python python-pip

Install Virtualenv and virtualenvwrapper

$ pip install virtualenv virtualenvwrapper
$ echo 'source /usr/local/bin/virtualenvwrapper.sh # Virtualenv/VirtualenvWrapper' >> ~/.bash_profile
$ source ~/.bash_profile

Create a virtual environment for the project
```
$ mkvirtualenv heart_rate
```
Note: This will install setuptools, pip and wheel modules in the new virtual environment.

Build

Move to the new virtual environment and change working directory to project's root
```
$ workon heart_rate
```
Note: To leave the virtual environment, execute
```
$ deactivate
```
Install dependencies
```
$ pip install -r requirements.txt
```
Install module
```
$ python setup.py clean --all install
```

Usage

The application can be run executing the heart_rate command. The following sections will explain the different options and arguments that can be used.

Displaying usage message

You can display the usage message using the -h or --help arguments. For example:

$ heart_rate --help

Displaying version number

You can check the version of the module using the -V or --version arguments. For example:

$ heart_rate -V

Logging verbosity

Logging levels

There are three levels of logging verbosity:

Normal
Verbose
Very Verbose.

Normal verbosity logging will log WARNING, ERROR and CRITICAL messages. Verbose logging will log what Normal logging logs, and INFO messages. Very Verbose logging is the same as Verbose logging, adding DEBUG messages.

Selecting a logging level

Normal Verbosity Logging

To use Normal verbosity logging just execute the command. Normal verbosity logging is the default

Verbose Logging

To use Verbose logging, add the -v or --verbose arguments. For example:

$ heart_rate --verbose

Very Verbose Logging

To use Very Verbose logging, add the -vv or --very-verbose arguments. For example:

$ heart_rate -vv

Setting video path

To set the video's path to analize, use the -vp or --video_path arguments. For example:

$ heart_rate -vp ~/video.mp4

The default value is the directory ./video.

Setting region of interest (ROI)

The rectangular region of interest consist of four limits. Each one specified by a parameter. This parameters are required and must be consistent, else the program will no work
To set the upper limit, use the -rUL or --roi-upper-limit argument. For example:

$ heart_rate -rUL 200

To set the lower limit, use the -rLL or --roi-lower-limit argument. For example:

$ heart_rate -rLL 250

To set the right limit, use the -rrL or --roi-right-limit argument. For example:

$ heart_rate -rrL 100

To set the left limit, use the -rlL or --roi-left-limit argument. For example:

$ heart_rate -rlL 150

Setting bandpass frequencies

To set the bandpass maximum frequency, use the -MF or --max-freq arguments. For example:

$ heart_rate --MF 7.0

The default value is 7.0.

To set the bandpass minimum frequency, use the -mF or --min-freq arguments. For example:

$ heart_rate --mF 0.4

The default value is 0.4.

Setting the channel to process

To set BLUE channel, use the -B or --blue arguments. For example:

$ heart_rate -B

To set RED channel, use the -R or --red arguments. For example:

$ heart_rate -R

To set GREEN channel, use the -G or --green arguments. For example:

$ heart_rate -G

The default channel is GREEN.

Example

Here is a full example usign all arguments:

$ heart_rate -rUL 600 -rLL 630 -rlL 300 -rrL 360  -mF 2.2 -MF 4.0 -G -vp videos/1_seg_120ppm.MOV

juanmbellini/heart_rate