CvSys

Module: tutorials.04_EM_tissue.10_cvsys.run

Section author: Christoph Augustin <christoph.augustin@medunigraz.at>

Introduction

This tutorial guides through using the 0D Cardiovascular system simulator. The code is based on the CircAdapt model, see [Arts2005], [Lumens2009], [Arts2012], and [Walmsley2015].

../../_images/circadapt_ode_system.png

Schematic of the 0D Closed-loop model CircAdapt

Usage

(Requires the cvsys package)

Basic Options

To see the full option list run

cvstool --help

The following basic options are available:

-h, --help              Display this information
-s, --solver <solver>   Choose ODE solver
                        Choices:
                          forw-euler: forward Euler method
                          rfk45: Runge-Kutta-Fehlberg 45
                          cvode: Sundials CVode solver
-d, --duration <float>  Duration of the simulation in (s)
                          default: 0.85 s
-o, --output <dir>      Place the output into the directory <dir>
--create-opts <file>    Create options file with default values
                          format choices are `json` and `prm`
                          default: `cvs_options.json`
--opts <file>           Use input options in <file>

The following command computes the heartbeat of a healthy adult over 60 seconds:

cvstool -d 60 \
        -o healthy_adult

Parameters of the cardiovascular systems can be changed using specific option files. First, generate options with

cvstool --create-opts cvs_options.json

Second, modify the options file cvs_options.json, e.g., set Aortic valve stenosis [pct.] to 70.

And third, simulate the heartbeat with a 70% aortic stenosis using the options file with

cvstool -d 60 \
        -o aortic_stenosis \
        --opts cvs_options.json

Post-processing

The cvsys experiment output information file on the cardiovascular system in the chosen output folder in csv format. Depending on the cardiovascular component these contain pressure information, volume information, flow rates and many other additional informations. These files can be used for a post-processing analysis using the tool cavplot. Call

cavplot --help

for a detailed description of the usage.

The default output containts pressure-volume loops as well as pressure and volume traces

cavplot ./healthy_adult/cav.LV.csv

To plot a time interval of the output use --time-interval or --time For example to plot the last two seconds of the simulation call

cavplot ./healthy_adult/cav.LV.csv --time-interval 58 60

To change the unit to mmHg use the flag --mmHg. To show PV loop and pressure traces for the aortic stenosis case call

cavplot ./aortic_stenosis/cav.LV.csv --time 58 --mmHg

This should give you a plot similar to

../../_images/cvsys_stenosis.png

cavplot output for the 70% stenosis case.

The options l+= and l= allow to add labels to the output. To compare the pvloops for the healthy case and the case with 70% aortic stenosis call

cavplot healthy_adult/cav.LV.csv:l="Healthy" \
        aortic_stenosis/cav.LV.csv:l="Aortic Stenosis" \
        --time 55 --pvloop
../../_images/cvsys_healthy_vs_stenosis.png

Pressure-volume plot comparing the healthy and the stenotic case.

The option ls= in {dotted, dashdot, dashed, solid} allows to change the linestyle. E.g., plot the pressure drop over the aortic valve:

cavplot aortic_stenosis/cav.LV.csv \
        aortic_stenosis/tube.AO.csv:ls=dashed \
        --time 55 --pressure
../../_images/cvsys_pressure_drop.png

Pressure-drop over the aortic valve.

The options v*=, p*=, and f*= allows to scale the volume(v), pressure(p), and flux(f), respectively. The same also works for \=, and +=, -= for a translation. E.g. plot the flux over the pulmonary outlet, the mitral valve, volume change of the left atrium in one plot:

cavplot aortic_stenosis/valve.PO.csv:f*=-1 \
        aortic_stenosis/valve.MV.csv \
        aortic_stenosis/cav.LA.csv:ls=dashed:l="LA Volume Change" \
        --flux --time 56.7 58.7
../../_images/cvsys_flux.png

Flux over pulmonary outlet and mitral valve and volume change of the left atrium.

Advanced Options

The following more advanced options are available:

--version <version>  Specify CircAdapt version to use (`2012`, `2015`)
                       default: `2015`
--no-peri            Run simulation without pericardium
--stiff-av-valves    Run simulation without updating leak area
                     of atrio-ventricular valves
--mass-conservation  Enable mass conservation
--allow-negative-p   Allow negative pressures in cavities

The different versions (2012, 2015) correspond to the publications [Arts2012] and [Walmsley2015], see also http://www.circadapt.org/downloads/files.

For example we can allow negative pressures in the cavities using

cvstool -d 60 -o healthy_adult_np --allow-negative-p

We plot the difference in the left atrial PV loop using the plotting option c= that allows to change the color using RGB-HEX format

cavplot healthy_adult/cav.LA.csv:l="standard":c=#000 \
        healthy_adult_np/cav.LA.csv:l="allow-negative-p":c=#ff0000 \
        --pvloop --time 55 --mmHg
../../_images/cvsys_neg_p.png

Left atrial pressure with the standard code in black and with the --allow-negative-p flag in red.

References

[Arts2005]T. Arts et al. AJP Heart 288 (2005): H1943-H1954. DOI: 10.1152/ajpheart.00444.2004.
[Arts2012](1, 2) T. Arts et al. PLoS Comput Biol 8 (2012): e1002369, DOI: 10.1371/journal.pcbi.1002369.
[Lumens2009]J. Lumens et al. Ann Biomed Eng 37 (2009): 2234-2255, DOI: 10.1007/s10439-009-9774-2.
[Walmsley2015](1, 2) J. Walmsley et al., PLoS Comput Biol 11 (2015): e1004284, DOI: 10.1371/journal.pcbi.1004284.