Sphinx Documentation of carputils Framework

`carputils.tools`

Functions for generating and executing openCARP command lines and other tools.

`tools.carp_cmd`([parfile, mech_symmetric])	Construct the basic openCARP command line.
`tools.carpexample`([parser, job_id, meshdir, …])	Generate a decorator for openCARP example run function.
`tools.standard_parser`([showdefault])	Generate a standard argument parser for collection of common options.
`tools.basic_parser`([showdefault, …])
`tools.gen_physics_opts`([ExtraTags, …])
`tools.basicexample`([parser, job_id, …])	Generate a decorator for openCARP example run function.

`carputils.job`

This package most importantly defines the Job class, which provides methods for executing bash commands.

Classes

job.Job(ID) A sequence of commands plus the tools to execute them.

`carputils.mesh`

Classes and routines for the generation of geometric meshes.

For a detailed description of how to use the mesh generation functionality, see carputils Mesh Generation.

Classes

`mesh.bivslice.BiVSlice`(r_lv, r_rv, …[, …])
`mesh.Block`([centre, size, resolution, …])	Generate a block mesh with the mesher command line utility.
`mesh.Cable`(x0, x1[, dx])	Generate a one dimensional mesh of line segments.
`mesh.Grid`(lowerleft, upperright[, …])	Generate a two dimensional mesh of a regular grid.
`mesh.Ring`(radius[, thickness, height, …])	Generate a mesh of a ring/cylindrical shell.
`mesh.Ellipsoid`(r_a, r_b, r_c[, aout, bout, …])	Generate a mesh of an ellipsoidal shell.
`mesh.BoxRegion`([lowerleft, upperright, tag, …])	Describe an axis-aligned cuboid for mesh tag assignment.
`mesh.pipe`	Generate a simple pipe geometry, providing a few parameters.
`mesh.SphereRegion`([radius, centre, tag, bath])	Describe a sphere for mesh tag assignment.
`mesh.CylinderRegion`([radius, start, axis, …])	Describe a cylinder for mesh tag assignment.

Functions

`mesh.generate`(geom[, dirname, rootdir])	Generate the specified geometry, unless it already exists.
`mesh.block_boundary_condition`(block, entity, …)	Generate a boundary condition definition for a `Block`.
`mesh.block_region`(block, entity, index, low, up)	Generate a boundary condition definition for a `Block`.
`mesh.linear_fibre_rule`(endo, epi[, unit])	Generate a linear fibre rule in the format expected by `carputils.mesh.Ring` and `carputils.mesh.Ellipsoid`.

`carputils.carpio`

Each module in this package defines a class for reading and writing a specific data type. Some convenience methods are also provided for common file type conversions.

`carputils.carpio.igb`

Provides a class for IGB IO to/from python numpy arrays.

Classes

igb.IGBFile(filename[, mode]) IGB format file IO class.

Functions

igb.open(*args, **kwargs) Open an IGB file.

`carputils.carpio.txt`

Provides a class for .dat and .vec IO to/from python numpy arrays.

Classes

txt.TxtFile(filename[, mode]) file IO class for reading ascii files with extensions - dat(.gz) - elem - vec(.gz) - vtx - pts

Functions

txt.open(*args, **kwargs) Open an .dat or .vec file.

`carputils.carpio.sv`

Functionality to read/write state variable (sv) files.

Classes

`sv.SVFile`(filename, dtype, dsize, bigendian)	Read a single state variable (sv) file.
`sv.SVSeries`()	Read a set of state variable (sv) files.

Functions

`sv.open`(args, *kwargs)	Read a state variable (sv) file
`sv.open_series`(args, *kwargs)	Read a state variable (sv) file series

`carputils.carpio.lut`

Read binary lookup tables into python numpy arrays

Classes

lut.LUTFile(filename) Read from a LUT file.

Functions

lut.open(*args, **kwargs) Open a LUT file.

`carputils.model`

Modules

`model.activetension`
`model.ionic`
`model.mechanics`

Classes

`model.ConductivityRegion`([IDs, name, g_il, …])	Defines an electrical conductivity region.
`model.EikonalRegion`(ID[, name, vel_f, …])	Defines an Eikonal model conduction velocity region.
`model.Stimulus`([name])	Represents a single stimulus argument to openCARP.

Functions

model.optionlist(components) Generate a list of command line options from the specified components.

`carputils.divertoutput`

Execute external processes with output buffering and error checking.

`divertoutput.call`(cmd[, interactive, …])	Run the specified command.
`divertoutput.subprocess_exceptions`()	Make `call()` raise an exception on process non-zero exit status.

`carputils.stream`

Some tools for handling output streams (stdout, etc.)

`stream.merge`(streams)	Merge the provided streams into a single one.
`stream.divert_std`(replacement)	Context manager to temporarily replace sys.stdout and sys.stderr.