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
- Attributes
procs (
list
) – list (N) of underlying interface elements to be processedproc_done (
numpy.ndarray
) – a boolean numpy array (N,) signifying whether a process has been submitted for executionproc_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 accross 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)¶ 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