nipype.pipeline.engine.workflows module¶
Defines functionality for pipelined execution of interfaces
The Workflow class provides core functionality for batch processing.
-
class
nipype.pipeline.engine.workflows.
Workflow
(name, base_dir=None)¶ Bases:
nipype.pipeline.engine.base.EngineBase
Controls the setup and execution of a pipeline of processes.
-
add_nodes
(nodes)¶ Add nodes to a workflow
- Parameters
nodes (list) – A list of EngineBase-based objects
-
clone
(name)¶ Clone a workflow
Note
Will reset attributes used for executing workflow. See _init_runtime_fields.
- Parameters
name (alphanumeric name) – unique name for the workflow
-
connect
(*args, **kwargs)¶ Connect nodes in the pipeline.
This routine also checks if inputs and outputs are actually provided by the nodes that are being connected.
Creates edges in the directed graph using the nodes and edges specified in the connection_list. Uses the NetworkX method DiGraph.add_edges_from.
- Parameters
args (list or a set of four positional arguments) –
Four positional arguments of the form:
connect(source, sourceoutput, dest, destinput)
source : nodewrapper node sourceoutput : string (must be in source.outputs) dest : nodewrapper node destinput : string (must be in dest.inputs)
A list of 3-tuples of the following form:
[(source, target, [('sourceoutput/attribute', 'targetinput'), ...]), ...]
Or:
[(source, target, [(('sourceoutput1', func, arg2, ...), 'targetinput'), ...]), ...] sourceoutput1 will always be the first argument to func and func will be evaluated and the results sent ot targetinput currently func needs to define all its needed imports within the function as we use the inspect module to get at the source code and execute it remotely
-
disconnect
(*args)¶ Disconnect nodes See the docstring for connect for format.
-
export
(filename=None, prefix='output', format='python', include_config=False)¶ Export object into a different format
- Parameters
filename (string) – file to save the code to; overrides prefix
prefix (string) – prefix to use for output file
format (string) – one of “python”
include_config (boolean) – whether to include node and workflow config values
-
get_node
(name)¶ Return an internal node by name
-
property
inputs
¶
-
list_node_names
()¶ List names of all nodes in a workflow
-
property
outputs
¶
-
remove_nodes
(nodes)¶ Remove nodes from a workflow
- Parameters
nodes (list) – A list of EngineBase-based objects
-
run
(plugin=None, plugin_args=None, updatehash=False)¶ Execute the workflow
- Parameters
plugin (plugin name or object) – Plugin to use for execution. You can create your own plugins for execution.
plugin_args (dictionary containing arguments to be sent to plugin) – constructor. see individual plugin doc strings for details.
-
write_graph
(dotfilename='graph.dot', graph2use='hierarchical', format='png', simple_form=True)¶ Generates a graphviz dot file and a png file
- Parameters
graph2use (‘orig’, ‘hierarchical’ (default), ‘flat’, ‘exec’, ‘colored’) – orig - creates a top level graph without expanding internal workflow nodes; flat - expands workflow nodes recursively; hierarchical - expands workflow nodes recursively with a notion on hierarchy; colored - expands workflow nodes recursively with a notion on hierarchy in color; exec - expands workflows to depict iterables
format (‘png’, ‘svg’)
simple_form (boolean (default: True)) – Determines if the node name used in the graph should be of the form ‘nodename (package)’ when True or ‘nodename.Class.package’ when False.
-
write_hierarchical_dotfile
(dotfilename=None, colored=False, simple_form=True)¶
-