carputils.tuning.CVtuning Class Reference

class for managing CV tuning More...

Public Member Functions
def	__init__ (self, vel=0.6, logfile='tuneCV.log', cvfile='results.dat', tablefile='table.dat')
def	config (self, args)
def	configCells (self)
	setup ionic model we want to use for CV tuning More...
def	hmean (self)
	Compute harmonic mean conductivity. More...
def	configConductivities (self)
	Define myocardial conductivities. More...
def	configNumerics (self)
	Define numerical settings for tuning experiment. More...
def	summary (self)
	Output summarized user settings. More...
def	carp_params (self)
def	report (self)
	fill dictionaries and output to log file More...
def	saveCVResults (self)
	write CV restitution results to .dat file More...
def	plotCVRestitutionCurve (self)
def	saveTuningResults (self)
	write tuning results to .dat file More...
def	geomStrand (self)
	Build strand-like FE mesh. More...
def	pcl2triggers (self)
	Turn pcl list into stimulus trigger list, assuming a first trigger at t start = 0. More...
def	configStimLHFace (self)
	Add stimulus definition to initiate propagation at the lhs face of the strand. More...
def	configStimLHFaceCarpentry (self)
	Add stimulus definition to initiate propagation at the lhs face of the strand in using stimulus[] rather than stim[] for backwards compatibility with carpentry. More...
def	configLATs (self)
	Set up detection of local activation times. More...
def	CV_obs_sites (self, rel_x)
	Extract spatial observation points for CV measurement. More...
def	measureCV (self, actsFile)
	Measure conduction velocity along a strand. More...
def	x_activated (self, o_lats, o_inds, pcl, siteID)
def	measureCVRes (self, actsFile)
	Measure conduction velocity along a strand. More...
def	buildCmd (self)
def	iterateCV (self, job)
def	restituteCV (self, job)

Public Attributes
	sres
	slen
	geom
	meshfiles
	surf
	model
	mpar
	plugin
	ppar
	svinit
	vel
	gi
	ge
	beta
	beqm
	conv
	ctol
	max_it
	pcl
	CVs
	vel_
	gi_
	ge_
	dt
	ts
	stol
	lump
	opsplt
	srcMod
	stimS
	stimV
	log
	last_it
	dat
	table
	cv_res
	visualize
	mode

Detailed Description

class for managing CV tuning

Parameters

Mesh parameters

sres float resolution of strand in um

slen float length of strand in cm

Ionic model parameters
----------------------

model name of ionic model default name is MBRDR

mpar model parameter list

default is empty

plugin : name of plugin

default is empty

ppar : plugin parameter list

default is empty

svinit : initial state vector file

default is empty

Tuning parameters

vel float desired velocity in m/s

gi float intracellular conductivity in S/m default is 0.174 S/m

ge float extracellular conductivity in S/m default is 0.625 S/m

beta float surface-to-volume ratio in 1/cm

beqm int switch between harmonic mean and intracellular monodomain tensor 0 intracellular monodomain tensor 1 bidomain equivalent harmonic mean monodomain tensor

conv bool converge to prescribed velocity

ctol float stop tolerance for CV tuning

Numerical parameters

dt float integration time step in us

ts int time stepping method 0 explicit 1 Crank-Nicolson

stol float solver tolerance

lump bool toggle mass lumping flag

opsplt bool toggle operator splitting flag

srcMod int select source model 0 monodomain 1 bidomain 2 pseudo-bidomain

Constructor & Destructor Documentation

__init__()

def carputils.tuning.CVtuning.__init__	(		self,
			vel = 0.6,
			logfile = 'tuneCV.log',
			cvfile = 'results.dat',
			tablefile = 'table.dat'
	)

Member Function Documentation

buildCmd()

def carputils.tuning.CVtuning.buildCmd

(

self

)

carp_params()

def carputils.tuning.CVtuning.carp_params

(

self

)

config()

def carputils.tuning.CVtuning.config	(		self,
			args
	)

configCells()

def carputils.tuning.CVtuning.configCells

(

self

)

setup ionic model we want to use for CV tuning

configConductivities()

def carputils.tuning.CVtuning.configConductivities

(

self

)

Define myocardial conductivities.

configLATs()

def carputils.tuning.CVtuning.configLATs

(

self

)

Set up detection of local activation times.

configNumerics()

def carputils.tuning.CVtuning.configNumerics

(

self

)

Define numerical settings for tuning experiment.

configStimLHFace()

def carputils.tuning.CVtuning.configStimLHFace

(

self

)

Add stimulus definition to initiate propagation at the lhs face of the strand.

configStimLHFaceCarpentry()

def carputils.tuning.CVtuning.configStimLHFaceCarpentry

(

self

)

Add stimulus definition to initiate propagation at the lhs face of the strand in using stimulus[] rather than stim[] for backwards compatibility with carpentry.

CV_obs_sites()

def carputils.tuning.CVtuning.CV_obs_sites	(		self,
			rel_x
	)

Extract spatial observation points for CV measurement.

geomStrand()

def carputils.tuning.CVtuning.geomStrand

(

self

)

Build strand-like FE mesh.

hmean()

def carputils.tuning.CVtuning.hmean

(

self

)

Compute harmonic mean conductivity.

iterateCV()

def carputils.tuning.CVtuning.iterateCV	(		self,
			job
	)

measureCV()

def carputils.tuning.CVtuning.measureCV	(		self,
			actsFile
	)

Measure conduction velocity along a strand.

As input the given mesh of a strand and the recorded activation times are used. Arrival times are computed at the interfaces of the quarters Q1/Q2 and Q3/Q4.

measureCVRes()

def carputils.tuning.CVtuning.measureCVRes	(		self,
			actsFile
	)

Measure conduction velocity along a strand.

As input the given mesh of a strand and the recorded activation times are used. Arrival times are computed at the interfaces of the quarters Q1/Q2 and Q3/Q4.

pcl2triggers()

def carputils.tuning.CVtuning.pcl2triggers

(

self

)

Turn pcl list into stimulus trigger list, assuming a first trigger at t start = 0.

plotCVRestitutionCurve()

def carputils.tuning.CVtuning.plotCVRestitutionCurve

(

self

)

report()

def carputils.tuning.CVtuning.report

(

self

)

fill dictionaries and output to log file

restituteCV()

def carputils.tuning.CVtuning.restituteCV	(		self,
			job
	)

saveCVResults()

def carputils.tuning.CVtuning.saveCVResults

(

self

)

write CV restitution results to .dat file

saveTuningResults()

def carputils.tuning.CVtuning.saveTuningResults

(

self

)

write tuning results to .dat file

summary()

def carputils.tuning.CVtuning.summary

(

self

)

Output summarized user settings.

x_activated()

def carputils.tuning.CVtuning.x_activated	(		self,
			o_lats,
			o_inds,
			pcl,
			siteID
	)

Member Data Documentation

beqm

carputils.tuning.CVtuning.beqm

beta

carputils.tuning.CVtuning.beta

conv

carputils.tuning.CVtuning.conv

ctol

carputils.tuning.CVtuning.ctol

cv_res

carputils.tuning.CVtuning.cv_res

CVs

carputils.tuning.CVtuning.CVs

dat

carputils.tuning.CVtuning.dat

dt

carputils.tuning.CVtuning.dt

ge

carputils.tuning.CVtuning.ge

ge_

carputils.tuning.CVtuning.ge_

geom

carputils.tuning.CVtuning.geom

gi

carputils.tuning.CVtuning.gi

gi_

carputils.tuning.CVtuning.gi_

last_it

carputils.tuning.CVtuning.last_it

log

carputils.tuning.CVtuning.log

lump

carputils.tuning.CVtuning.lump

max_it

carputils.tuning.CVtuning.max_it

meshfiles

carputils.tuning.CVtuning.meshfiles

mode

carputils.tuning.CVtuning.mode

model

carputils.tuning.CVtuning.model

mpar

carputils.tuning.CVtuning.mpar

opsplt

carputils.tuning.CVtuning.opsplt

pcl

carputils.tuning.CVtuning.pcl

plugin

carputils.tuning.CVtuning.plugin

ppar

carputils.tuning.CVtuning.ppar

slen

carputils.tuning.CVtuning.slen

srcMod

carputils.tuning.CVtuning.srcMod

sres

carputils.tuning.CVtuning.sres

stimS

carputils.tuning.CVtuning.stimS

stimV

carputils.tuning.CVtuning.stimV

stol

carputils.tuning.CVtuning.stol

surf

carputils.tuning.CVtuning.surf

svinit

carputils.tuning.CVtuning.svinit

table

carputils.tuning.CVtuning.table

ts

carputils.tuning.CVtuning.ts

vel

carputils.tuning.CVtuning.vel

vel_

carputils.tuning.CVtuning.vel_

visualize

carputils.tuning.CVtuning.visualize

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The documentation for this class was generated from the following file:

• carputils/tuning.py