Myokit

https://myokit.readthedocs.io
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Myokit is a Python library and tool designed for modeling and simulation of cardiac cellular...
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### myokit video command syntax and examples

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/util.rst.txt

Commands for the myokit video tool. The first shows the general syntax, the second a concrete example converting results.zip to movie.mp4, and the third displays the full syntax help.

```bash
$ myokit video <inputfile> <variable> -dst <outputfile>
```

```bash
$ myokit video results.zip membrane.V -dst movie.mp4
```

```bash
$ myokit video --help
```

--------------------------------

### myokit opencl example output

Source: https://myokit.readthedocs.io/en/stable/cmd/system.html

Example output of the myokit opencl command, showing platform and device details.

```text
Platform 0
 Current id : 22734896
 Name       : Intel(R) OpenCL
 Vendor     : Intel(R) Corporation
 Version    : OpenCL 1.2 LINUX
 Profile    : FULL_PROFILE
 Extensions : cl_khr_fp64 cl_khr_icd
 Devices    :
  Device 0
   Current id      : 21277656
   Name            : Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz
   Vendor          : Intel(R) Corporation
   Version         : OpenCL 1.2 (Build 67279)
   Driver          : 1.2
   Clock speed     : 2500 MHz
   Global memory   : 7870 MB
   Local memory    : 32 KB
   Constant memory : 128 KB
   Max work groups : 1024
   Max work items  : [1024, 1024, 1024]
   Max param size  : 3840 bytes

```

--------------------------------

### Example output of myokit version

Source: https://myokit.readthedocs.io/en/stable/cmd/system.html

Example output of the `myokit version` command, showing the version number with decorative ASCII art.

```text
 Myokit version 1.21.0         |/\
_______________________________|  |______

```

--------------------------------

### myokit import: syntax and examples

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Imports a model definition or protocol using any available importer. The syntax is shown, followed by examples with and without an output file. If no output file is specified, the generated mmt file is printed to the screen.

```bash
$ myokit import <format> <source_file> -o <output_file>

```

```bash
$ myokit import cellml example.cellml

```

```bash
$ myokit import cellml example.cellml test.mmt

```

--------------------------------

### Run myokit compiler

Source: https://myokit.readthedocs.io/en/stable/cmd/system.html

Tests the locally installed compiler by compiling a small test module that queries the system for the installed compiler.

```bash
$ myokit compiler

```

--------------------------------

### myokit export: syntax and examples

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Exports an mmt file using any available exporter. The syntax is shown, followed by examples for converting to CellML and creating runnable C code.

```bash
$ myokit export <exporter_name> <source_file> <output_directory>

```

```bash
$ myokit export cellml example.mmt example.cellml

```

```bash
$ myokit export ansic example.mmt example_in_c

```

--------------------------------

### Run Myokit command line utility

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/index.rst.txt

Two equivalent ways to launch the Myokit command line utility: using the Python module invocation or the installed script. The first works from the myokit directory, the second from anywhere if Myokit was installed with pip or setup.py.

```bash
$ python -m myokit
```

```bash
$ myokit
```

--------------------------------

### size() examples: log entries and resulting sizes

Source: https://myokit.readthedocs.io/en/stable/api_simulations/DataLog.html

Examples for size(). The first two show that size is the number of entries, not the maximum index. The third shows a two-dimensional size (2,3). The last shows a global variable with size ().

```text
0.membrane.V
1.membrane.V
2.membrane.V
```

```text
0.membrane.V
10.membrane.V
20.membrane.V
```

```text
0.0.membrane.V
0.1.membrane.V
0.2.membrane.V
1.0.membrane.V
1.1.membrane.V
1.2.membrane.V
```

```text
engine.time
```

--------------------------------

### myokit.OpenCL.selection_info()

Source: https://myokit.readthedocs.io/en/stable/api_simulations/SimulationOpenCL.html

Static method to get a list of platform/device combinations for selection.

```APIDOC
## myokit.OpenCL.selection_info()

### Description
Returns a list of platform/device combinations along with information allowing the user to select one. The returned output is a list of tuples, where each tuple has the form `(platform_name, device_name, specs)`. A preferred device can be selected by passing one of the returned `platform_name, device_name` combinations to `OpenCL.set_preferred_device()`.

### Method
Static method

### Signature
`myokit.OpenCL.selection_info()`

### Parameters
None

### Returns
- **list** - A list of tuples `(platform_name, device_name, specs)`.
```

--------------------------------

### Debug overview example: a = 10, b = 5 * a, c = b^2

Source: https://myokit.readthedocs.io/en/stable/_sources/guide/exploring.rst.txt

Shows the output of the Ctrl-D debug feature when the cursor points at a variable. The example uses a = 10, b = 5 * a, and c = b^2, and the debug overview for c displays the expressions used to evaluate it.

```text
a = 10
b = 5 * a
c = b^2
```

--------------------------------

### myokit video: generate movies from DataBlock files

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Generates movies from DataBlock1d or DataBlock2d files. Requires moviepy to be installed. The syntax is shown, followed by an example command.

```bash
$ myokit video <inputfile> <variable> -dst <outputfile>

```

```bash
$ myokit video results.zip membrane.V -dst movie.mp4

```

--------------------------------

### myokit compare --help: show full syntax

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Displays the full command-line syntax for the compare tool.

```bash
$ myokit compare --help

```

--------------------------------

### Check unit conversion with myokit.lib.multi.unit

Source: https://myokit.readthedocs.io/en/stable/api_library/multi.html

Shows how to use multi.unit to check if a variable's unit can be converted to a target unit and get the conversion factor. In this example, a millivolt is converted to volts, yielding 0.001. Raises myokit.IncompatibleModelError if conversion is not possible.

```python
>>> import myokit
>>> import myokit.lib.multi as multi
>>> m,p,x = myokit.load('example')
>>> print(multi.unit(m.label('membrane_potential'), myokit.units.V))
0.001
```

--------------------------------

### Show step help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/util.rst.txt

Displays the full syntax for the step command.

```bash
$ myokit step --help
```

--------------------------------

### Voltage clamp protocol using the 'next' keyword

Source: https://myokit.readthedocs.io/en/stable/_sources/syntax/protocol.rst.txt

Rewrites the voltage clamp example using 'next' to denote the start time as the end of the previous event. Times specified with 'next' are rounded to 9 digits to avoid floating point summation errors.

```myokit
[[protocol]]
#level  start   length  period  multiplier
-80     0       500     0       0
 40     next    500     0       0
-80     next    1000    1000    0
```

--------------------------------

### Using Component.get() to retrieve variables

Source: https://myokit.readthedocs.io/en/stable/api_core/Component.html

Shows how to use the get() method on a component to retrieve variables by name. The example loads a model, retrieves the component 'ina', then retrieves variable 'h' using a relative name. Attempting to use a fully qualified name like 'ina.h' raises a KeyError because names are relative to the component.

```python
>>> import myokit
>>> m = myokit.load_model('example')
>>> c = m.get('ina')        # Retrieves the component <ina>
>>> h = c.get('h')          # Retrieves the variable <ina.h>
>>> x = c.get('ina.h')      # Searches for <ina.ina.h>: KeyError!
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
KeyError: 'ina'
```

--------------------------------

### myokit import --help: show full syntax

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Displays the full command-line syntax for the import tool.

```bash
$ myokit import --help

```

--------------------------------

### myokit run --help: show full syntax

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Displays the full command-line syntax for the run tool.

```bash
$ myokit run --help

```

--------------------------------

### start()

Source: https://myokit.readthedocs.io/en/stable/api_simulations/Protocol.html

Returns the time this event starts.

```APIDOC
## start()

### Description
Returns the time this event starts.

### Method
N/A (method call)

### Endpoint
N/A

### Parameters
None

### Returns
Start time (number)
```

--------------------------------

### Show myokit ide help

Source: https://myokit.readthedocs.io/en/stable/cmd/gui.html

Displays the full syntax for the `ide` command.

```bash
$ myokit ide --help

```

--------------------------------

### myokit compiler

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/system.rst.txt

Tests the local compiler installation by compiling a small test module that queries the system for the installed compiler.

```APIDOC
## `myokit compiler`

### Description
Tests the local compiler installation by compiling a small test module that queries the system for the installed compiler.

### Usage
```
myokit compiler [--debug]
```

### Options
- `--debug` (optional) - Provides more information if compilation is unsuccessful.

### Example
```
$ myokit compiler
```

### Example Output
```
Compilation successful. Found: GCC 11.2.1
```
```

--------------------------------

### myokit video --help: show full syntax

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Displays the full command-line syntax for the video tool.

```bash
$ myokit video --help

```

--------------------------------

### myokit step --help: show full syntax

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Displays the full command-line syntax for the step tool.

```bash
$ myokit step --help

```

--------------------------------

### Show import help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/util.rst.txt

Displays the full syntax for the import command.

```bash
$ myokit import --help
```

--------------------------------

### Show run help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/util.rst.txt

Displays the full syntax for the run command.

```bash
$ myokit run --help
```

--------------------------------

### keys() example: log entries

Source: https://myokit.readthedocs.io/en/stable/api_simulations/DataLog.html

Example log entries for keys(). The iterator produces keys in the order shown, with the second index changing fastest.

```text
0.0.membrane.V
1.0.membrane.V
0.1.membrane.V
1.1.membrane.V
0.2.membrane.V
1.2.membrane.V
```

--------------------------------

### ProgressPrinter output example

Source: https://myokit.readthedocs.io/en/stable/api_simulations/LongSimulations.html

Example of the output printed to stdout by ProgressPrinter during a simulation. Shows the elapsed time, percentage done, and estimated remaining time.

```text
[8.9 minutes] 71.7 % done, estimated 4.2 minutes remaining
```

--------------------------------

### Show Myokit help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/index.rst.txt

Displays a full overview of all available Myokit command line subcommands.

```bash
$ myokit -h
```

--------------------------------

### Example SimulationError output

Source: https://myokit.readthedocs.io/en/stable/_sources/api_simulations/SimulationErrors.rst.txt

Example output from a SimulationError. It shows the time and cell where the error occurred, the state before and during the error, the expression being evaluated, and the operands that caused the invalid value.

```text
Encountered numerical error at t=411.054992676 in cell (55) when membrane.V=-77.0.
Obtained 4 previous state(s).
State before:
membrane.V = -77.0
ina.m      =  5.76317822560667992e-03
ina.h      =  3.50723683834075928e-01
ina.j      =  1.33311852812767029e-01
ica.d      =  6.89173266291618347e-02
ica.f      =  7.21855103969573975e-01
ik.x       =  3.83078485727310181e-01
ica.Ca_i   =  2.27514933794736862e-03
State during:
membrane.V = nan
ina.m      =  5.75887179002165794e-03
ina.h      =  3.50991368293762207e-01
ina.j      =  1.33416950702667236e-01
ica.d      =  6.88845962285995483e-02
ica.f      =  7.21879780292510986e-01
ik.x       =  3.83071571588516235e-01
ica.Ca_i   =  2.27477238513529301e-03
Evaluating derivatives at state before...
invalid value encountered in float_scalars
Encountered when evaluating
  if(membrane.V < -100.0, 1.0, 2.837 * (exp(0.04 * (membrane.V + 77.0))
                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

        - 1.0) / ((membrane.V + 77.0) * exp(0.04 * (membrane.V + 35.0))))
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

With the following operands:
  (1) 0.0
  (2) 0.0
And the following variables:
  membrane.V = -77.0
             = -77.0
```

--------------------------------

### Show myokit opencl help

Source: https://myokit.readthedocs.io/en/stable/cmd/system.html

Shows the full syntax for the myokit opencl command.

```bash
$ myokit opencl --help

```

--------------------------------

### Install shortcut icons with myokit icons

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/system.rst.txt

Installs shortcut icons on Linux or Windows. On Linux, also creates the .mmt mime-type and registers Myokit to handle .mmt and other file types.

```bash
$ myokit icons
```

--------------------------------

### Show compare help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/util.rst.txt

Displays the full syntax for the compare command.

```bash
$ myokit compare --help
```

--------------------------------

### Example log output for multi-cell simulation

Source: https://myokit.readthedocs.io/en/stable/api_simulations/SimulationOpenCL.html

Example of the data log structure returned by the OpenCL simulation when logging 'engine.time' and 'membrane.V' for multiple cells. The cell index is prefixed to the variable name.

```python
{
    'engine.time'  : [...],
    '0.membrane.V' : [...],
    '1.membrane.V' : [...],
    '2.membrane.V' : [...],
}

```

--------------------------------

### Show ide help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/gui.rst.txt

Displays the full syntax and options for the ``ide`` command.

```console
$ myokit ide --help
```

--------------------------------

### ids() example: log entries and returned ids

Source: https://myokit.readthedocs.io/en/stable/api_simulations/DataLog.html

Example log entries for a two-dimensional variable and the corresponding ids returned by ids(). The ids are tuples of indices, with the second index changing fastest.

```text
0.0.membrane.V
0.1.membrane.V
0.2.membrane.V
1.0.membrane.V
1.1.membrane.V
1.2.membrane.V
```

```text
[(0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2)]
```

--------------------------------

### myokit.OpenCL.info(formatted=False)

Source: https://myokit.readthedocs.io/en/stable/api_simulations/SimulationOpenCL.html

Static method to query the OpenCL installation for available platforms and devices.

```APIDOC
## myokit.OpenCL.info(formatted=False)

### Description
Queries the OpenCL installation for the available platforms and devices and returns a `myokit.OpenCLInfo` object. If `formatted=True` is set, a formatted version of the information is returned instead.

### Method
Static method

### Signature
`myokit.OpenCL.info(formatted=False)`

### Parameters
- **formatted** (bool) - Optional - If `True`, a formatted string version of the information is returned instead of an `OpenCLInfo` object.

### Returns
- **myokit.OpenCLInfo** - Information about all available OpenCL platforms and devices.
- **str** - Formatted string version of the information if `formatted=True`.
```

--------------------------------

### Show myokit log help

Source: https://myokit.readthedocs.io/en/stable/cmd/gui.html

Displays the full syntax for the `log` command.

```bash
$ myokit log --help

```

--------------------------------

### Print system information with myokit system

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/system.rst.txt

Retrieves and prints system information useful for debugging a Myokit installation, including Myokit version, Python version, OS, and installed Python packages.

```bash
$ myokit system
```

```text
== System information ==
Myokit: 1.35.0
Python: 3.11.3 (main, May 24 2023, 00:00:00) [GCC 12.3.1 20230508 (Red Hat 12.3.1-1)]

OS: Linux (linux, posix)
    Linux-6.3.5-100.fc37.x86_64-x86_64-with-glibc2.36

== Python requirements ==
NumPy: 1.24.3
SciPy: 1.8.1
Matplotlib: 3.6.3
ConfigParser: OK
Setuptools: 62.6.0

== Python extras ==
SymPy: 1.11.1
MoviePy: 1.0.3
```

--------------------------------

### Example log output for a 3-cell simulation

Source: https://myokit.readthedocs.io/en/stable/api_simulations/Simulation1d.html

Example output log structure when running a 3-cell simulation with the given log arguments. Time-bound variables are logged globally, while per-cell variables are prefixed with the cell index.

```python
{
    'engine.time'  : [...],
    '0.membrane.V' : [...],
    '1.membrane.V' : [...],
    '2.membrane.V' : [...],
}
```

--------------------------------

### walk() example output

Source: https://myokit.readthedocs.io/en/stable/api_core/expressions.html

Shows the depth-first traversal order of the expression tree for `5 + (2 * sqrt(x))`, as returned by the walk() method. The output lists each node in the order visited.

```text
5 + (2 * sqrt(x))

1) Plus
2) Number(5)
3) Multiply
4) Number(2)
5) Sqrt
6) Name(x)

```

--------------------------------

### Show log help

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/gui.rst.txt

Displays the full syntax and options for the ``log`` command.

```console
$ myokit log --help
```

--------------------------------

### Launch log command

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/gui.rst.txt

Launches the Myokit DataLog Viewer. Example usage without arguments.

```console
$ myokit log
```

--------------------------------

### default_state_sensitivities()

Source: https://myokit.readthedocs.io/en/stable/api_simulations/Simulation.html

Method to get default sensitivities.

```APIDOC
## default_state_sensitivities()

### Description
Returns the default sensitivities with respect to state variables, or None if sensitivities are not enabled.

### Method
default_state_sensitivities()

### Returns
- **sensitivities** (object or None) - The default sensitivities, or None.
```

--------------------------------

### importers

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Function to get available importers.

```APIDOC
## importers()

### Description
Returns a dict of all importers available in this module.

### Returns
- `dict` - A dictionary of importers.
```

--------------------------------

### myokit export --help: show full syntax

Source: https://myokit.readthedocs.io/en/stable/cmd/util.html

Displays the full command-line syntax for the export tool.

```bash
$ myokit export --help

```

--------------------------------

### AtfFile.filename

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the ATF filename.

```APIDOC
## filename()

### Description
Returns this ATF's filename.

### Returns
- `str` - The filename of the ATF file.
```

--------------------------------

### Channel.unit

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the channel units.

```APIDOC
## unit()

### Description
Returns the units this channel is in.

### Returns
- `myokit.Unit` - The units of the channel.
```

--------------------------------

### Benchmarker usage example

Source: https://myokit.readthedocs.io/en/stable/api_core/tools.html

Creates a Benchmarker, runs a simulation, prints the elapsed time, resets the timer, runs again, and prints a formatted time string.

```python
m,p,x = myokit.load('example')
s = myokit.Simulation(m, p)
b = myokit.tools.Benchmarker()
s.run()
print(b.time())
b.reset()
s.run()
print(b.format())

```

--------------------------------

### Channel.name

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the channel name.

```APIDOC
## name()

### Description
Returns the name set for this channel.

### Returns
- `str` - The name of the channel.
```

--------------------------------

### Show myokit block help

Source: https://myokit.readthedocs.io/en/stable/cmd/gui.html

Displays the full syntax for the `block` command.

```bash
$ myokit block --help

```

--------------------------------

### Channel.index

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the channel index.

```APIDOC
## index()

### Description
Returns the index set for this channel.

### Returns
- `int` - The index of the channel.
```

--------------------------------

### Step with reference and initial values

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/util.rst.txt

Tests with different initial values by including an additional file.

```bash
$ myokit step example.mmt -ref ref_step.txt -ini ref_init.txt
```

--------------------------------

### version

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the version number.

```APIDOC
## version()

### Description
Returns a string representation of this file's version number.

### Returns
- `str` - The version number as a string.
```

--------------------------------

### Launch block command

Source: https://myokit.readthedocs.io/en/stable/_sources/cmd/gui.rst.txt

Launches the DataBlock Viewer. Example usage without arguments.

```console
$ myokit block
```

--------------------------------

### time_unit

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the time unit.

```APIDOC
## time_unit()

### Description
Returns the time unit used in this source.

### Returns
- `myokit.Unit` - The time unit.
```

--------------------------------

### sweep_count

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get the number of sweeps.

```APIDOC
## sweep_count()

### Description
Returns the number of sweeps. Note that a source with zero recorded channels may still report a non-zero number of sweeps if it can provide D/A outputs. Similarly, formats like WCP can report zero sweeps but have a non-zero channel count (if no data was recorded).

### Returns
- `int` - The number of sweeps.
```

--------------------------------

### Launch Myokit IDE with myokit ide

Source: https://myokit.readthedocs.io/en/stable/cmd/gui.html

Launches the Myokit IDE with no arguments.

```bash
$ myokit ide

```

--------------------------------

### Example output of myokit opencl-select

Source: https://myokit.readthedocs.io/en/stable/cmd/system.html

Shows the output produced by the opencl-select command, including the current selection and a list of available devices with a prompt to select one.

```text
Loading Myokit...
======================================================================
Myokit OpenCL device selection
======================================================================
Selected platform: No preference
Selected device  : No preference
======================================================================
Available devices:
----------------------------------------------------------------------
(1) Select automatically.
----------------------------------------------------------------------
(2) Platform: NVIDIA CUDA
    Device: GeForce GT 640
    901 MHz, 3.9 GB global, 48.0 KB local, 64.0 KB const
----------------------------------------------------------------------
Please select an OpenCL device by typing 1 or 2
Leave blank to keep current selection.
Select device:

```

--------------------------------

### meta_str

Source: https://myokit.readthedocs.io/en/stable/api_formats/axon.html

Method to get metadata as a string.

```APIDOC
## meta_str(_show_header=False_)

### Description
Returns a multi-line string with meta data about this file. The optional argument `show_header` can be used to add the full header contents to the output.

### Parameters
- **show_header** (bool) - Optional - If `True`, include the full header contents. Default is `False`.

### Returns
- `str` - Multi-line string with meta data.
```
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