carputils.forcepss.j2carp Namespace Reference

Classes
class	SweepSetup
class	LeadfieldComputationOptions

Functions
def	load_json (file_name)
def	print_subdict (key, val, shift_num=0)
def	print_settings_config (config, config_header=False)
def	save_json (jdata, file_name, indent=2, overwrite=True)
def	write_vtx_file (filename, vtx_list)
def	write_carp_par_file (filename, opts, start_num=1)
def	valid_keys (jsec, key_lst)
def	get_init_dir (init_dir, up)
	Retrieve/create path to initialization directory. More...
def	is_mutable (sec, ignore)
def	vel2List (CVs, G)
def	get_bath_labels (cnf, pop=False)
def	ep_secs_to_carp (cnf, fncs, use_abs_paths=True)
def	ep_sec_to_carp (tags, key, ep, idx, use_abs_paths=True)
def	G_secs_to_carp (cnf, fncs, ek=False, dream=False)
def	G_sec_to_carp (tags, key, G, idx, cv_ref=None)
def	CV_secs_to_carp (cnf, fncs)
def	CV_sec_to_carp (cv, idx, key)
def	gen_physics (ExtraTags=None, IntraTags=None, EikonalTags=None, MechTags=None, FluidTags=None)
def	domain_to_phys_region (ptype, name, domain, idx)
def	elec_sec_to_carp (job, elecs, idx, act_lst, *model_name=None, model_format=None, ucc_file=None, stim_filename=None, dry=False)
def	get_ground_stimulus (lfsetup, ground_vtx_file, stim_num, dry=False)
def	stim_sec_to_carp (job, stimuli, lfsetup, rmode, output_dir, **kwargs)
def	get_elec_point (pt, pt_idx, stm)
def	mgquery_idx_call (job, spec_line, stim_name, model_name, model_format, ucc_file, dry=False)
def	build_stim_geom (job, elec, idx, stm_name, *model_name=None, model_format=None, ucc_file=None, stim_filename=None, dry=False)
def	ek_lat_detect (idx, threshold=-10, **kwargs)
def	lat (idx, ID, threshold=-10, measurand=0, mode=0, detect_all=0, method=1)
def	sentinel (idx, start, window)
def	propagation_mode (mode)
def	setup_mesh (meshname, use_split=True, split_file=None, tags_file=None)
	Set up mesh command including the use of a split file as well as an alternative element tag vector. More...
def	intra_mesh_ext (rmode)
def	setup_tissue (cnf, fncs, rmode, **kwargs)
def	check_config (cnf, fncs)
def	add_slv_settings (slv)
def	setup_timings (plan)
def	check_initial_state_vectors (funcs, verbose)
def	update_exp_desc (up_flag, exp_file, exp, indent=2)
def	generate_split_file (job, plan, mesh_name, force_recreation=False)
def	plan2carp (job, plan_file, meshname, rmode)
def	check_stim_protocol (config, check_type='stimulus')

Variables
bool	SA_AVAILABLE = False
bool	UQ_AVAILABLE = False
string	CONFIGURATIONS = 'config'
string	CONFIGURATION_FUNC = 'func'
string	CONFIGURATION_TAGS = 'tags'
string	FUNCTIONS = 'functions'
string	FUNCTION_CV = 'CV'
string	FUNCTION_CV_CVMEAS = 'CVmeas'
string	FUNCTION_CV_CVREF = 'CVref'
string	FUNCTION_CV_COND = 'G'
string	FUNCTION_EP = 'EP'
string	FUNCTION_EP_MODEL = 'model'
string	FUNCTION_EP_MODELPAR = 'modelpar'
string	FUNCTION_EP_BCL = 'bcl'
string	FUNCTION_EP_INIT = 'init'
string	FUNCTION_EP_CYCLES = 'cycles'
string	FUNCTION_EP_PLUGINS = 'plugins'
string	FUNCTION_EP_PLUGPARS = 'plugin-par'
string	FUNCTION_EP_APDRESFILE = 'apdres'
string	FUNCTION_EP_APDRESPRTCL = 'apdresptcl'
tuple	FUNCTION_CV_COND_ACTIVE_NAMES = ('gil', 'git', 'gin', 'gel', 'get', 'gen')
string	FUNCTION_CV_COND_PASSIVE_NAMES = 'gbath'
tuple	FUNCTION_CV_VELOCITY_NAMES = ('vf', 'vs', 'vn')
string	ELECTRODES = 'electrodes'
string	ELECTRODE_TYPE = 'type'
string	SIMULATION = 'simulation'
string	STIMULATION_STIMULI = 'stimuli'
string	STIMULATION_TYPE = 'type'
string	STIMULATION_ELECTRODE = 'electrode'
string	STIMULATION_PROTOCOL = 'protocol'
string	STIMULATION_STRENGTH = 'strength'
dictionary	STIMULATION_TYPE_MAP
string	SPLIT = 'split'
string	SPLIT_OPSTR = 'opstr'
string	SPLIT_APPLY = 'apply'
string	LFSETUP = 'lfsetup'
string	SOLVER = 'solver'
string	SOLVER_DT = 'dt'
string	SOLVER_DX = 'dx'
string	SOLVER_PARABSOLVE = 'ts'
string	SOLVER_MASSLUMPING = 'lumping'
string	SOLVER_OPSPLIT = 'opsplit'
string	SOLVER_CGTOL = 'stol'
string	SOLVER_BEQM = 'beqm'
string	SOLVER_FIXGE = 'fixge'
string	SOLVER_SRC_MODEL = 'sourceModel'
string	PROTOCOLS = 'protocols'
string	PROTOCOLS_BCL = 'bcl'
string	PROTOCOLS_CYCLES = 'cycles'
string	PROTOCOLS_ELECTRODES = 'electrodes'
string	PROTOCOLS_PROPAGATION = 'propagation'
string	PROTOCOLS_LATFILE = 'lat'
string	PROTOCOLS_PREPACE = 'prepace'
string	PROTOCOLS_RESTART = 'restart'
string	PROTOCOLS_RELTIMINGS = 'rel-timings'
string	PROTOCOLS_APD_RESTITUTION = 'APD-restitution'
string	PROTOCOLS_APD_RESTITUTION_TYPE = 'type'
string	PROTOCOLS_APD_RESTITUTION_BCL = 'bcl'
string	PROTOCOLS_APD_RESTITUTION_CI0 = 'CI0'
string	PROTOCOLS_APD_RESTITUTION_CI1 = 'CI1'
string	PROTOCOLS_APD_RESTITUTION_PPBEATS = 'pp_beats'
string	PROTOCOLS_APD_RESTITUTION_PMBEATS = 'pm_beats'
string	PROTOCOLS_APD_RESTITUTION_PMDEC = 'pm_dec'
list	SAMPLING_METHODS = ['file']

Function Documentation

add_slv_settings()

def carputils.forcepss.j2carp.add_slv_settings

(

slv

)

build_stim_geom()

def carputils.forcepss.j2carp.build_stim_geom	(		job,
			elec,
			idx,
			stm_name,
		*	model_name = None,
			model_format = None,
			ucc_file = None,
			stim_filename = None,
			dry = False
	)

check_config()

def carputils.forcepss.j2carp.check_config	(		cnf,
			fncs
	)

check_initial_state_vectors()

def carputils.forcepss.j2carp.check_initial_state_vectors	(		funcs,
			verbose
	)

check_stim_protocol()

def carputils.forcepss.j2carp.check_stim_protocol	(		config,
			check_type = 'stimulus'
	)

CV_sec_to_carp()

def carputils.forcepss.j2carp.CV_sec_to_carp	(		cv,
			idx,
			key
	)

CV_secs_to_carp()

def carputils.forcepss.j2carp.CV_secs_to_carp	(		cnf,
			fncs
	)

domain_to_phys_region()

def carputils.forcepss.j2carp.domain_to_phys_region	(		ptype,
			name,
			domain,
			idx
	)

ek_lat_detect()

def carputils.forcepss.j2carp.ek_lat_detect	(		idx,
			threshold = -10,
		**	kwargs
	)

elec_sec_to_carp()

def carputils.forcepss.j2carp.elec_sec_to_carp	(		job,
			elecs,
			idx,
			act_lst,
		*	model_name = None,
			model_format = None,
			ucc_file = None,
			stim_filename = None,
			dry = False
	)

ep_sec_to_carp()

def carputils.forcepss.j2carp.ep_sec_to_carp	(		tags,
			key,
			ep,
			idx,
			use_abs_paths = True
	)

ep_secs_to_carp()

def carputils.forcepss.j2carp.ep_secs_to_carp	(		cnf,
			fncs,
			use_abs_paths = True
	)

G_sec_to_carp()

def carputils.forcepss.j2carp.G_sec_to_carp	(		tags,
			key,
			G,
			idx,
			cv_ref = None
	)

G_secs_to_carp()

def carputils.forcepss.j2carp.G_secs_to_carp	(		cnf,
			fncs,
			ek = False,
			dream = False
	)

gen_physics()

def carputils.forcepss.j2carp.gen_physics	(		ExtraTags = None,
			IntraTags = None,
			EikonalTags = None,
			MechTags = None,
			FluidTags = None
	)

generate_split_file()

def carputils.forcepss.j2carp.generate_split_file	(		job,
			plan,
			mesh_name,
			force_recreation = False
	)

get_bath_labels()

def carputils.forcepss.j2carp.get_bath_labels	(		cnf,
			pop = False
	)

get_elec_point()

def carputils.forcepss.j2carp.get_elec_point	(		pt,
			pt_idx,
			stm
	)

get_ground_stimulus()

def carputils.forcepss.j2carp.get_ground_stimulus	(		lfsetup,
			ground_vtx_file,
			stim_num,
			dry = False
	)

get_init_dir()

def carputils.forcepss.j2carp.get_init_dir	(		init_dir,
			up
	)

Retrieve/create path to initialization directory.

Parameters

init_dir
up

Returns

path to directory for storing initialization files (state vectors, lat sequences, checkpoints, ...)

intra_mesh_ext()

def carputils.forcepss.j2carp.intra_mesh_ext

(

rmode

)

is_mutable()

def carputils.forcepss.j2carp.is_mutable	(		sec,
			ignore
	)

lat()

def carputils.forcepss.j2carp.lat	(		idx,
			ID,
			threshold = -10,
			measurand = 0,
			mode = 0,
			detect_all = 0,
			method = 1
	)

load_json()

def carputils.forcepss.j2carp.load_json

(

file_name

)

mgquery_idx_call()

def carputils.forcepss.j2carp.mgquery_idx_call	(		job,
			spec_line,
			stim_name,
			model_name,
			model_format,
			ucc_file,
			dry = False
	)

plan2carp()

def carputils.forcepss.j2carp.plan2carp	(		job,
			plan_file,
			meshname,
			rmode
	)

print_settings_config()

def carputils.forcepss.j2carp.print_settings_config	(		config,
			config_header = False
	)

print_subdict()

def carputils.forcepss.j2carp.print_subdict	(		key,
			val,
			shift_num = 0
	)

propagation_mode()

def carputils.forcepss.j2carp.propagation_mode

(

mode

)

save_json()

def carputils.forcepss.j2carp.save_json	(		jdata,
			file_name,
			indent = 2,
			overwrite = True
	)

sentinel()

def carputils.forcepss.j2carp.sentinel	(		idx,
			start,
			window
	)

setup_mesh()

def carputils.forcepss.j2carp.setup_mesh	(		meshname,
			use_split = True,
			split_file = None,
			tags_file = None
	)

Set up mesh command including the use of a split file as well as an alternative element tag vector.

Parameters

meshname
use_split
split_file
tags_file

Returns

mesh_opts command line parameters for selecting mesh, split file and alternative tag vector

setup_timings()

def carputils.forcepss.j2carp.setup_timings

(

plan

)

setup_tissue()

def carputils.forcepss.j2carp.setup_tissue	(		cnf,
			fncs,
			rmode,
		**	kwargs
	)

stim_sec_to_carp()

def carputils.forcepss.j2carp.stim_sec_to_carp	(		job,
			stimuli,
			lfsetup,
			rmode,
			output_dir,
		**	kwargs
	)

update_exp_desc()

def carputils.forcepss.j2carp.update_exp_desc	(		up_flag,
			exp_file,
			exp,
			indent = 2
	)

valid_keys()

def carputils.forcepss.j2carp.valid_keys	(		jsec,
			key_lst
	)

vel2List()

def carputils.forcepss.j2carp.vel2List	(		CVs,
			G
	)

write_carp_par_file()

def carputils.forcepss.j2carp.write_carp_par_file	(		filename,
			opts,
			start_num = 1
	)

write_vtx_file()

def carputils.forcepss.j2carp.write_vtx_file	(		filename,
			vtx_list
	)

Variable Documentation

CONFIGURATION_FUNC

string carputils.forcepss.j2carp.CONFIGURATION_FUNC = 'func'

CONFIGURATION_TAGS

string carputils.forcepss.j2carp.CONFIGURATION_TAGS = 'tags'

CONFIGURATIONS

string carputils.forcepss.j2carp.CONFIGURATIONS = 'config'

ELECTRODE_TYPE

string carputils.forcepss.j2carp.ELECTRODE_TYPE = 'type'

ELECTRODES

string carputils.forcepss.j2carp.ELECTRODES = 'electrodes'

FUNCTION_CV

string carputils.forcepss.j2carp.FUNCTION_CV = 'CV'

FUNCTION_CV_COND

string carputils.forcepss.j2carp.FUNCTION_CV_COND = 'G'

FUNCTION_CV_COND_ACTIVE_NAMES

tuple carputils.forcepss.j2carp.FUNCTION_CV_COND_ACTIVE_NAMES = ('gil', 'git', 'gin', 'gel', 'get', 'gen')

FUNCTION_CV_COND_PASSIVE_NAMES

string carputils.forcepss.j2carp.FUNCTION_CV_COND_PASSIVE_NAMES = 'gbath'

FUNCTION_CV_CVMEAS

string carputils.forcepss.j2carp.FUNCTION_CV_CVMEAS = 'CVmeas'

FUNCTION_CV_CVREF

string carputils.forcepss.j2carp.FUNCTION_CV_CVREF = 'CVref'

FUNCTION_CV_VELOCITY_NAMES

tuple carputils.forcepss.j2carp.FUNCTION_CV_VELOCITY_NAMES = ('vf', 'vs', 'vn')

FUNCTION_EP

string carputils.forcepss.j2carp.FUNCTION_EP = 'EP'

FUNCTION_EP_APDRESFILE

string carputils.forcepss.j2carp.FUNCTION_EP_APDRESFILE = 'apdres'

FUNCTION_EP_APDRESPRTCL

string carputils.forcepss.j2carp.FUNCTION_EP_APDRESPRTCL = 'apdresptcl'

FUNCTION_EP_BCL

string carputils.forcepss.j2carp.FUNCTION_EP_BCL = 'bcl'

FUNCTION_EP_CYCLES

string carputils.forcepss.j2carp.FUNCTION_EP_CYCLES = 'cycles'

FUNCTION_EP_INIT

string carputils.forcepss.j2carp.FUNCTION_EP_INIT = 'init'

FUNCTION_EP_MODEL

string carputils.forcepss.j2carp.FUNCTION_EP_MODEL = 'model'

FUNCTION_EP_MODELPAR

string carputils.forcepss.j2carp.FUNCTION_EP_MODELPAR = 'modelpar'

FUNCTION_EP_PLUGINS

string carputils.forcepss.j2carp.FUNCTION_EP_PLUGINS = 'plugins'

FUNCTION_EP_PLUGPARS

string carputils.forcepss.j2carp.FUNCTION_EP_PLUGPARS = 'plugin-par'

FUNCTIONS

string carputils.forcepss.j2carp.FUNCTIONS = 'functions'

LFSETUP

string carputils.forcepss.j2carp.LFSETUP = 'lfsetup'

PROTOCOLS

string carputils.forcepss.j2carp.PROTOCOLS = 'protocols'

PROTOCOLS_APD_RESTITUTION

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION = 'APD-restitution'

PROTOCOLS_APD_RESTITUTION_BCL

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_BCL = 'bcl'

PROTOCOLS_APD_RESTITUTION_CI0

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_CI0 = 'CI0'

PROTOCOLS_APD_RESTITUTION_CI1

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_CI1 = 'CI1'

PROTOCOLS_APD_RESTITUTION_PMBEATS

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_PMBEATS = 'pm_beats'

PROTOCOLS_APD_RESTITUTION_PMDEC

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_PMDEC = 'pm_dec'

PROTOCOLS_APD_RESTITUTION_PPBEATS

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_PPBEATS = 'pp_beats'

PROTOCOLS_APD_RESTITUTION_TYPE

string carputils.forcepss.j2carp.PROTOCOLS_APD_RESTITUTION_TYPE = 'type'

PROTOCOLS_BCL

string carputils.forcepss.j2carp.PROTOCOLS_BCL = 'bcl'

PROTOCOLS_CYCLES

string carputils.forcepss.j2carp.PROTOCOLS_CYCLES = 'cycles'

PROTOCOLS_ELECTRODES

string carputils.forcepss.j2carp.PROTOCOLS_ELECTRODES = 'electrodes'

PROTOCOLS_LATFILE

string carputils.forcepss.j2carp.PROTOCOLS_LATFILE = 'lat'

PROTOCOLS_PREPACE

string carputils.forcepss.j2carp.PROTOCOLS_PREPACE = 'prepace'

PROTOCOLS_PROPAGATION

string carputils.forcepss.j2carp.PROTOCOLS_PROPAGATION = 'propagation'

PROTOCOLS_RELTIMINGS

string carputils.forcepss.j2carp.PROTOCOLS_RELTIMINGS = 'rel-timings'

PROTOCOLS_RESTART

string carputils.forcepss.j2carp.PROTOCOLS_RESTART = 'restart'

SA_AVAILABLE

bool carputils.forcepss.j2carp.SA_AVAILABLE = False

SAMPLING_METHODS

list carputils.forcepss.j2carp.SAMPLING_METHODS = ['file']

SIMULATION

string carputils.forcepss.j2carp.SIMULATION = 'simulation'

SOLVER

string carputils.forcepss.j2carp.SOLVER = 'solver'

SOLVER_BEQM

string carputils.forcepss.j2carp.SOLVER_BEQM = 'beqm'

SOLVER_CGTOL

string carputils.forcepss.j2carp.SOLVER_CGTOL = 'stol'

SOLVER_DT

string carputils.forcepss.j2carp.SOLVER_DT = 'dt'

SOLVER_DX

string carputils.forcepss.j2carp.SOLVER_DX = 'dx'

SOLVER_FIXGE

string carputils.forcepss.j2carp.SOLVER_FIXGE = 'fixge'

SOLVER_MASSLUMPING

string carputils.forcepss.j2carp.SOLVER_MASSLUMPING = 'lumping'

SOLVER_OPSPLIT

string carputils.forcepss.j2carp.SOLVER_OPSPLIT = 'opsplit'

SOLVER_PARABSOLVE

string carputils.forcepss.j2carp.SOLVER_PARABSOLVE = 'ts'

SOLVER_SRC_MODEL

string carputils.forcepss.j2carp.SOLVER_SRC_MODEL = 'sourceModel'

SPLIT

string carputils.forcepss.j2carp.SPLIT = 'split'

SPLIT_APPLY

string carputils.forcepss.j2carp.SPLIT_APPLY = 'apply'

SPLIT_OPSTR

string carputils.forcepss.j2carp.SPLIT_OPSTR = 'opstr'

STIMULATION_ELECTRODE

string carputils.forcepss.j2carp.STIMULATION_ELECTRODE = 'electrode'

STIMULATION_PROTOCOL

string carputils.forcepss.j2carp.STIMULATION_PROTOCOL = 'protocol'

STIMULATION_STIMULI

string carputils.forcepss.j2carp.STIMULATION_STIMULI = 'stimuli'

STIMULATION_STRENGTH

string carputils.forcepss.j2carp.STIMULATION_STRENGTH = 'strength'

STIMULATION_TYPE

string carputils.forcepss.j2carp.STIMULATION_TYPE = 'type'

STIMULATION_TYPE_MAP

dictionary carputils.forcepss.j2carp.STIMULATION_TYPE_MAP

Initial value:

=  {'Transmembrane Current': 0,
                        'Transmembrane Voltage clamp': 9,
                        'extracellular current': 1,
                        'extracellular voltage (closed loop)': 2,
                        'extracellular ground': 3,
                        'intracellular current': 4,
                        'extracellular voltage (open loop)': 5,
                        'prescribed takeoff': 8,
                        'Vm clamp': 9,
                        'prescribed phie': 10}

UQ_AVAILABLE

bool carputils.forcepss.j2carp.UQ_AVAILABLE = False