nest package

Subpackages

• nest.lib package
  • Submodules
  • nest.lib.hl_api_connections module
  • nest.lib.hl_api_helper module
  • nest.lib.hl_api_info module
  • nest.lib.hl_api_models module
  • nest.lib.hl_api_nodes module
  • nest.lib.hl_api_parallel_computing module
  • nest.lib.hl_api_simulation module
  • nest.lib.hl_api_subnets module
  • Module contents
• nest.tests package
  • Subpackages
    • nest.tests.test_sp package
      • Submodules
      • nest.tests.test_sp.mpitest_issue_578_sp module
      • nest.tests.test_sp.test_all module
      • nest.tests.test_sp.test_conn_builder module
      • nest.tests.test_sp.test_disconnect module
      • nest.tests.test_sp.test_disconnect_multiple module
      • nest.tests.test_sp.test_enable_multithread module
      • nest.tests.test_sp.test_get_sp_status module
        • Structural Plasticity GetStatus Test
      • nest.tests.test_sp.test_growth_curves module
      • nest.tests.test_sp.test_sp_manager module
      • nest.tests.test_sp.test_synaptic_elements module
      • nest.tests.test_sp.test_update_synaptic_elements module
      • nest.tests.test_sp.utils module
      • Module contents
  • Submodules
  • nest.tests.compatibility module
  • nest.tests.test_aeif_lsodar module
  • nest.tests.test_all module
  • nest.tests.test_connect_all_patterns module
  • nest.tests.test_connect_all_to_all module
  • nest.tests.test_connect_array_fixed_indegree module
  • nest.tests.test_connect_array_fixed_outdegree module
  • nest.tests.test_connect_distributions module
  • nest.tests.test_connect_fixed_indegree module
  • nest.tests.test_connect_fixed_outdegree module
  • nest.tests.test_connect_fixed_total_number module
  • nest.tests.test_connect_helpers module
  • nest.tests.test_connect_one_to_one module
  • nest.tests.test_connect_pairwise_bernoulli module
  • nest.tests.test_connect_parameters module
  • nest.tests.test_connect_symmetric_pairwise_bernoulli module
  • nest.tests.test_create module
  • nest.tests.test_csa module
  • nest.tests.test_current_recording_generators module
  • nest.tests.test_dataconnect module
  • nest.tests.test_erfc_neuron module
  • nest.tests.test_errors module
  • nest.tests.test_events module
  • nest.tests.test_facetshw_stdp module
  • nest.tests.test_getconnections module
  • nest.tests.test_helper_functions module
  • nest.tests.test_labeled_synapses module
  • nest.tests.test_mc_neuron module
  • nest.tests.test_networks module
  • nest.tests.test_onetooneconnect module
  • nest.tests.test_parrot_neuron module
  • nest.tests.test_parrot_neuron_ps module
  • nest.tests.test_pp_psc_delta module
  • nest.tests.test_pp_psc_delta_stdp module
  • nest.tests.test_quantal_stp_synapse module
  • nest.tests.test_rate_copy_model module
  • nest.tests.test_rate_instantaneous_and_delayed module
  • nest.tests.test_rate_neuron module
  • nest.tests.test_rate_neuron_communication module
  • nest.tests.test_refractory module
  • nest.tests.test_siegert_neuron module
  • nest.tests.test_split_simulation module
  • nest.tests.test_stack module
  • nest.tests.test_status module
  • nest.tests.test_stdp_multiplicity module
  • nest.tests.test_stdp_triplet_synapse module
  • nest.tests.test_threads module
  • nest.tests.test_use_gid_in_filename module
  • nest.tests.test_vogels_sprekeler_synapse module
  • nest.tests.test_weight_recorder module
  • Module contents

Submodules

nest.raster_plot module

Functions for raster plotting.

nest.raster_plot.extract_events(data, time=None, sel=None)

Extract all events within a given time interval.

Both time and sel may be used at the same time such that all events are extracted for which both conditions are true.

data : list

Matrix such that data[:,0] is a vector of all gids and data[:,1] a vector with the corresponding time stamps.

time : list, optional

List with at most two entries such that time=[t_max] extracts all events with t< t_max time=[t_min, t_max] extracts all events with t_min <= t < t_max

sel : list, optional

List of gids such that sel=[gid1, … , gidn] extracts all events from these gids. All others are discarded.

numpy.array

List of events as (gid, t) tuples

nest.raster_plot.from_data(data, sel=None, **kwargs)

Plot raster plot from data array.

data : list

Matrix such that data[:,0] is a vector of all gids and data[:,1] a vector with the corresponding time stamps.

sel : list, optional

List of gids such that sel=[gid1, … , gidn] extracts all events from these gids. All others are discarded.

kwargs:

Parameters passed to _make_plot

nest.raster_plot.from_device(detec, plot_lid=False, **kwargs)

Plot raster from a spike detector.

detec : TYPE

Description

plot_lid : bool, optional

Whether to convert from local IDs

kwargs:

Parameters passed to _make_plot

nest.NESTError

nest.raster_plot.from_file(fname, **kwargs)

Plot raster from file.

fname : str or tuple(str) or list(str)

File name or list of file names

If a list of files is given, the data from them is concatenated as if it had been stored in a single file - useful when MPI is enabled and data is logged separately for each MPI rank, for example.

kwargs:

Parameters passed to _make_plot

nest.raster_plot.from_file_numpy(fname, **kwargs)

Use numpy.

nest.raster_plot.from_file_pandas(fname, **kwargs)

Use pandas.

nest.visualization module

nest.voltage_trace module

Functions to plot voltage traces.

nest.voltage_trace.from_device(detec, neurons=None, title=None, grayscale=False, timeunit='ms')

Plot the membrane potential of a set of neurons recorded by the given Voltmeter or Multimeter.

detec : list

Global id of Voltmeter or Multimeter in a list, e.g. [1]

neurons : list, optional

Indices of of neurons to plot

title : str, optional

Plot title

grayscale : bool, optional

Plot in grayscale

timeunit : str, optional

Unit of time

nest.NESTError

Description

nest.voltage_trace.from_file(fname, title=None, grayscale=False)

Plot voltage trace from file.

fname : str or list

Filename or list of filenames to load from

title : str, optional

Plot title

grayscale : bool, optional

Plot in grayscale

ValueError

nest.voltage_trace.show()

Call pylab.show() to show all figures and enter the GUI main loop. Python will block until all figure windows are closed again. You should call this function only once at the end of a script.

See also: http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show

Module contents

Initializer of PyNEST.

nest.catching_sli_run(cmd)

Send a command string to the NEST kernel to be executed, catch SLI errors and re-raise them in Python.

cmd : str

The SLI command to be executed.

NESTError

SLI errors are bubbled to the Python API as NESTErrors.

nest.init(argv)

Initializes NEST.

argv : list

Command line arguments, passed to the NEST kernel

_kernel.NESTError

nest.pcd()

nest.sli_func(s, *args, **kwargs)

Convenience function for executing an SLI command s with arguments args.

This executes the SLI sequence: sli_push(args); sli_run(s); y=sli_pop()

s : str

Function to call

*args

Arbitrary number of arguments to pass to the SLI function

**kwargs

namespace : str

The sli code is executed in the given SLI namespace.

litconv : bool

Convert string args beginning with / to literals.

The function may have multiple return values. The number of return values is determined by the SLI function that was called.

r,q = sli_func(‘dup rollu add’,2,3) r = sli_func(‘add’,2,3) r = sli_func(‘add pop’,2,3) l = sli_func(‘CreateLayer’, {…}, namespace=’topology’)

nest.sli_pop()

nest.sli_push()

nest.sli_run(cmd)

Send a command string to the NEST kernel to be executed, catch SLI errors and re-raise them in Python.

cmd : str

The SLI command to be executed.

NESTError

SLI errors are bubbled to the Python API as NESTErrors.

nest.spp()

nest.sps()

nest.sr(cmd)

Send a command string to the NEST kernel to be executed, catch SLI errors and re-raise them in Python.

cmd : str

The SLI command to be executed.

NESTError

SLI errors are bubbled to the Python API as NESTErrors.

nest.test()

Runs all PyNEST unit tests.