nipype.pipeline.plugins.base module¶
Common graph operations for execution.
- class nipype.pipeline.plugins.base.DistributedPluginBase(plugin_args=None)¶
Bases:
nipype.pipeline.plugins.base.PluginBase
Execute workflow with a distribution engine
Combinations of
proc_done
andproc_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 across 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)¶
Bases:
nipype.pipeline.plugins.base.PluginBase
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 objectupdatehash (
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 objectupdatehash (
bool
) – whether cached nodes with stale hash should be just updated.
- class nipype.pipeline.plugins.base.SGELikeBatchManagerBase(template, plugin_args=None)¶
Bases:
nipype.pipeline.plugins.base.DistributedPluginBase
Execute workflow with SGE/OGE/PBS like batch system