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

Attributes:

procs (list) – list (N) of underlying interface elements to be processed
proc_done (numpy.ndarray) – a boolean numpy array (N,) signifying whether a process has been submitted for execution
proc_pending (numpy.ndarray) – a boolean numpy array (N,) signifying whether a process is currently running.
depidx (numpy.matrix) – a boolean matrix (NxN) storing the dependency structure across processes. Process dependencies are derived from each column.

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