nipype.pipeline.plugins.base module¶

Common graph operations for execution.

class nipype.pipeline.plugins.base.DistributedPluginBase(plugin_args=None)¶

Execute workflow with a distribution engine

Combinations of proc_done and proc_pending:

proc_done	proc_pending	outcome
True	False	Process is finished
True	True	Process is currently being run
False	False	Process is queued
False	True	INVALID COMBINATION

procs¶

list (N) of underlying interface elements to be processed

Type:	`list`

proc_done¶

a boolean numpy array (N,) signifying whether a process has been submitted for execution

Type:	`numpy.ndarray`

proc_pending¶

a boolean numpy array (N,) signifying whether a process is currently running.

Type:	`numpy.ndarray`

depidx¶

a boolean matrix (NxN) storing the dependency structure accross processes. Process dependencies are derived from each column.

Type:	`numpy.matrix`

run(graph, config, updatehash=False)¶: Executes a pre-defined pipeline using distributed approaches

class nipype.pipeline.plugins.base.GraphPluginBase(plugin_args=None)¶

Base class for plugins that distribute graphs to workflows

run(graph, config, updatehash=False)¶

Instruct the plugin to execute the workflow graph.

The core plugin member that should be implemented by all plugins.

Parameters:	graph – a networkx, flattened DAG to be executed config (`config`) – a nipype.config object updatehash (`bool`) – whether cached nodes with stale hash should be just updated.

class nipype.pipeline.plugins.base.PluginBase(plugin_args=None)¶

Bases: object

Base class for plugins.

run(graph, config, updatehash=False)¶

Instruct the plugin to execute the workflow graph.

The core plugin member that should be implemented by all plugins.

Parameters:	graph – a networkx, flattened DAG to be executed config (`config`) – a nipype.config object updatehash (`bool`) – whether cached nodes with stale hash should be just updated.

class nipype.pipeline.plugins.base.SGELikeBatchManagerBase(template, plugin_args=None)¶

Execute workflow with SGE/OGE/PBS like batch system