Installation¶

Packaged Program Install¶

For our most recently released version, visit our GitHub release page.
Select our most recent release.
In the asset section, download the packaged zip file.
Once the file is downloaded, unzip the file.

Source Install¶

Install Python3¶

Install Python Dependencies¶

Activate Python virtual environment to help manage package installation.

#Posix
python3 -m venv <venv>
source <venv>/bin/activate

#Windows
python3 -m venv <venv>
<venv>/Scripts/activate.bat

Install dependencies; a list of all dependencies can also be found below.

pip install -r requirements.txt

Python Dependencies¶
Package	Application	Program Module Utilization
argparse	This library collects arguments that are provided in the command line when executing the script so that they can be easily accessed as variables	SASSI
csv	This library assists with reading in data from csv files such as the metadata and auto_criteria settings files	SASSI
datetime	This library provides a data structure for handling dates and times and applying mathematic operations to them - this is used as part of the logging system for tracking events through the execution of the script	SASSI
logging	This library aids in generating contextualized logging feedback to the console as well as the log file	SASSI
lmxl	This package is used in the ReadMe word document generation to access content within configuration .csv files.	GUI
math	This library provides additional functions for numerical operations and is currently used to aid in verifying if N/A values are present	SASSI
numpy	This library includes several classes and functions that are used including arrays for storing values as well as mathematic and filtering generating functions	SASSI, GUI
os	This library provides access to functions for file i/o and filepath creationg and parsing	SASSI
pandas	This library is used for its DataFrame class that is used to store several variables including the input signals and the detected breaths and their derived parameters. Several methods that act upon DataFrame are utilized for filtering and applying calculations to the data.	SASSI, GUI
pyodbc	This library provides methods and utilities for accessing ODBC databases in Python	GUI
PyQt5	This library is used for rendering graphics and GUI components like buttons and input boxes. It also manages processes that run parallel to the main GUI thread.	GUI
PyQt5-Qt5	This library is a subset of a Qt installation that is required by PyQt5	GUI
PyQt5-sip	This library provides Python bindings for C/C++ in support of PyQt5	GUI
python-dateutil	This library extends the Python native package datetime with extra utilities for working with dates and times	GUI
python-docx	This library is used to render word documents that summarize user selections for STAGG runs.	GUI
pytz	This library provides Olson timezone calculations	GUI
re	This library is used for regular expression parsing of text strings and is used for parsing MUID and PlyUID information	SASSI
scipy	This library provides functions used for signal processing including high and low pass filters that are used to reduce noise in the derived flow signal. Additionally, this library’s `linregress` function is used for the creation of calibration curves (O2 and CO2 concentrations vs. voltages).	SASSI, GUI
six	This library provides smooth compatibility between libraries written for both Python 2 and Python 3	GUI
statistics	This library is used to provide access to statistical functions such as median	SASSI
sys	This library is used to connect the systems stdout to logging functions, used for displaying logging messages in the console	SASSI
tkinter	This library is used to provide a minimal GUI when running the SASSI script separately from the GUI	SASSI

Install R¶

Install R here.

Install R Dependencies¶

All required packages and dependencies for R are automatically downloaded and installed upon the first run of STAGG.
Manual package installation can be done inside of the R terminal using

install.packages("<package_name>", dependencies = TRUE)

or each individual package can be installed through the command line via CRAN with

wget https://cran.r-project.org/src/contrib/<package_name_and_version>.tar.gz
R CMD INSTALL <package_name_and_version>.tar.gz

Note

Note that the latter method does not automatically install package dependencies. The list of required packages is below.

Producing the R markdown also requires an installation of pandocs; instructions can be found here.

R Dependencies¶
Package	Application
argparser	Allows for operation of the R module, STAGG, from the command line terminal
data.table	Reformatting of data tables in preparation for manipulations
ggpubr	Graphing and data visualization
ggthemes	Additional settings and configurations for graphing
kableExtra	Builds common complex tables and manipulates table styles
lme4	Fits linear and generalized linear mized-effects models
lmerTest	Provides p-values for linear mixed-effects models
magrittr	Improves readability and intuitiveness of code
multcomp	Fits linear mixed-effects models and multiple comparisons
openxlsx	Reads, writes, and edits xlsx files
pandoc	Used for R markdown rendering
RColorBrewer	Generates colors for graphing
reshape2	Used to transform data table formats for some optional graphs
rjson	Allows import of JSON formatted files
rmarkdown	Produces html summary file with all .svg output files in one page
svglite	Produces user-friendly editable .svg image files
tidyselect	Allows verbiage consistency between packages
tidyverse	Data management and formatting; include dplyr and ggplot2 packages
xtable	Generates tables from functional outputs

Launching Breathe Easy¶

From packaged version¶

Inside the unzipped file, you’ll find a folder named SASSI-STAGG_QUIPPL.
Double click the launcher.bat file in this folder to launch the GUI.
1. The launcher.bat file can be moved to your Desktop or another easily accessible location on your computer to make the program easy to access later.

From source¶

#Posix
source venv/bin/activate
python3 scripts/GUI/MainGUImain.py

#Windows
<venv>/Scripts/activate.bat
python3 scripts/GUI/MainGUImain.py