I need to process a simulation that was acquired using FE Bio $($of an LV$).$ Below are the directions, deliverables, and helpful hints. I will also attach an image of what the final graph should look like.

Import all the $.$csv files into MATLAB $($or Python$)$

Identify the nodes on the periphery of the LV on the base plane to calculate the centroid.

Convert the triangle information $($the node numbers$)$ to coordinates using the position file and find the volume $($for all steps$)$ using the tetrahedron method described in class.

Extract the pressure values on the triangles associated with the LV and take the average $($again$,$ for all the steps$).$

Plot the Pressure $($in mmHg$)$ vs Volume $($in micro Liter$)$

Files required: $.$feb $($geometry$),$ position.csv$,$ and pressure.csv

Copy all nodes and elements from the $.$feb file and store them in arrays.

Nodes $=[$x coordinate, y coordinate, z coordinate$]$

Elements $=[$Elem$\_$ID$,$ Node$\_$ID $1,$ Node$\_$ID $2,$ Node$\_$ID $3,$ Node$\_$ID $4]$

Extract nodes and faces belonging to the LV endocardium from the $.$feb file

i$.$e$.,$ the faces on which the LV pressure is applied.

Endo$\_$Faces $=[$Node$\_$ID $1,$ Node$\_$ID $2,$ Node$\_$ID $3]$

Endo$\_$Nodes $=$ stack$($unique$($Endo$\_$Faces$))$

Find corresponding elements.

for face in Endo$\_$Faces:

if $2$ or $3$ Nodes of face in Elements:

Endo$\_$Elements $=$ stack$($Elem$\_$ID$)$

Endo$\_$Elements $=$ unique$($Endo$\_$Elements$)$

Extracting pressure $($element data$)$ and volume $($node data$)$ for each

time point.

pressure $=[$Elem$\_$ID$,$ t$1,$ t$2,....$ tn$]$

position $=[$Node$\_$ID$,$ xt$1,$ yt$1,$ zt$1,$ xt$2,$ yt$2,$ zt$2,....,$

xtn$,$ ytn$,$ ztn$]$

for time$\_$point in tn:

endo$\_$pressure $=[]$

endo$\_$volume $=[]$

for i in size$($pressure$,1)$:

if pressure$($i$,0)$ in Endo$\_$Elements:

endo$\_$pressure $=$ stack$($pressure$,$time$\_$point$)$

Endo$\_$Pressure$\_$average $=$ mean$($endo$\_$pressure$)$

for i in size$($position$,1)$:

if position$($i$,0)$ in Endo$\_$Nodes:

endo$\_$position $=$ stack$($x$\_$time$\_$point, y$\_$time$\_$point, z$\_$time$\_$point$)$

centroid $=$ mean$($endo$\_$position$[$base nodes$])$

position$\_$vector $=$ endo$\_$position $-$ centroid

for face in Endo$\_$Faces:

Tet$\_$Volume $=(1/6)*($position$\_$vector$($Node$\_$ID $1)$ x position$\_$vector$($Node$\_$ID $2)).($position$\_$vector$($Node$\_$ID $2)$ x position$\_$vector$($Node$\_$ID $3))$

Tet$\_$Volume $=$ stack$($Tet$\_$Volume$)$

Endo$\_$Volume$\_$Total $=$ sum$($Tet$\_$Volume$)$

Helpful commands

MATLAB: readmatrix, vertcat, horzcat, unique, mean, sum, cross, dot

Python: numpy.genfromtxt, numpy.vstack, numpy.hstack, numpy.sum

numpy.unique, numpy.mean, numpy.cross, numpy.dot