brian2tools.nmlexport.supporting module

class brian2tools.nmlexport.supporting.NeuroMLPoissonGenerator(poissid, average_rate)

Bases: object

Makes XML of spikeGeneratorPoisson for NeuroML2/LEMS simulation.

build()

Builds NeuroML DOM structure of spikeGeneratorPoisson and returns it.

Returns:generator – DOM representation of generator. Return type:xml.minidom.dom

class brian2tools.nmlexport.supporting.NeuroMLSimpleNetwork(id_)

Bases: object

NeuroMLSimpleNetwork class representing network tag in NeuroML syntax as a XML DOM representation.

add_component(id_, type_, **attributes)

Adds a component to a network.

Parameters:

• id (str) – component id
• type (str) – type of component
• attributes (.., optional) – more attributes

build()

Builds NeuroML DOM structure of network. It returns DOM object.

Returns:network – DOM representation of network. Return type:xml.minidom.dom

class brian2tools.nmlexport.supporting.NeuroMLSimulation(simid, target, length='1s', step='0.1ms')

Bases: object

NeuroMLSimulation class representing Simulation tag in NeuroML syntax as a XML DOM representation.

add_display(dispid, title='', time_scale='1ms', xmin='0', xmax='1000', ymin='0', ymax='11')

Adds a Display element to Simulation.

Parameters:

• dispid (str) – display id
• title (str) – title printed on display window
• time_scale (str) – time scale of a plot
• xmax, ymin, ymax (xmin,) – limits of plot

add_eventoutputfile(outfileid, filename='recordings.spikes', format_='TIME_ID')

Adds an EventOutputFile element to a recently added Display.

Parameters:

• outfileid (str) – EventOutputFile id
• filename (str) – name of an output file
• format (str, optional) – format of data storage, default TIME_ID

add_eventselection(esid, select, event_port='spike')

Adds an EventSelection element to a recently added EventOutputFile.

Parameters:

• esid (str) – EventSelection id
• select (str) – index of selected neuron
• event_port (str) – event port name, default ‘spike’

add_line(linid, quantity, scale='1mV', time_scale='1ms')

Adds a Line element to a recently added Display.

Parameters:

• linid (str) – line id
• quantity (str) – measure to plot
• scale (str) – scale of a function
• time_scale (str) – time scale of a line

add_outputcolumn(ocid, quantity)

Adds an OutputColumn element to a recently added OutputFile tag.

Parameters:

• ocid (str) – OutputColumn id
• quantity (str) – measure to store in a column

add_outputfile(outfileid, filename='recordings.dat')

Adds an OutputFile to Simulation.

Parameters:

• outfileid (str) – OutputFile id
• filename (str) – name of an output file

build()

Builds NeuroML DOM structure of Simulation. It returns DOM object or it can be accessed by object.simulation.

Returns:simulation – DOM representation of simulation. Return type:xml.minidom.dom

create_simulation(simid, target, length, step)

Adds a Simulation element to DOM structure at init.

Parameters:

• simid (str) – simulation id.
• target (str) – target NeuroML object: component or network
• length (str, optional) – length of simulation, default 1 sec
• step (str, optional) – step of integration, default 0.1 ms

update_simulation_attribute(attr_name, attr_value)

Updates simulation attributes.

Parameters:

• attr_name (str) – attribute name
• attr_value (str or int or float) – attribute value

class brian2tools.nmlexport.supporting.NeuroMLTarget(component)

Bases: object

Makes XML of target of NeuroML2/LEMS simulation.

build()

Builds NeuroML DOM structure of target and returns it.

Returns:target – DOM representation of target. Return type:xml.minidom.dom

brian2tools.nmlexport.supporting.brian_unit_to_lems(valunit)

Returns string representation of LEMS unit where * is between value and unit e.g. “20. mV” -> “20.*mV”.

Parameters:valunit (Quantity or str) – text or brian2.Quantity representation of a value with unit Returns:valstr – string representation of LEMS unit Return type:str

brian2tools.nmlexport.supporting.from_string(rep)

Returns Quantity object from text representation of a value.

Parameters:rep (str) – text representation of a value with unit Returns:q – Brian Quantity object Return type:Quantity

brian2tools.nmlexport.supporting.read_nml_dims(nmlcdpath='')

Read from NeuroMLCoreDimensions.xml all supported by LEMS dimensions and store it as a Python dict with name as a key and Brian2 unit as value.

Parameters:nmlcdpath (str, optional) – Path to ‘NeuroMLCoreDimensions.xml’ Returns:lems_dimenssions – Dictionary with LEMS dimensions. Return type:dict

brian2tools.nmlexport.supporting.read_nml_units(nmlcdpath='')

Read from ‘NeuroMLCoreDimensions.xml’ all supported by LEMS units.

Parameters:nmlcdpath (str, optional) – Path to ‘NeuroMLCoreDimensions.xml’ Returns:lems_units – List with LEMS units. Return type:list