API

The exact API of all functions and classes, as given by the docstrings.

User guide: See the User Guide section for further details.

capsul.pipeline: Pipeline

Pipeline Definition

pipeline.Pipeline([autoexport_nodes_parameters]) Pipeline containing Process nodes, and links between node parameters.

Node Types

pipeline_nodes.Node(pipeline, name, inputs, ...) Basic Node structure of the pipeline that need to be tuned.
pipeline_nodes.ProcessNode(pipeline, name, ...) Process node.
pipeline_nodes.PipelineNode(pipeline, name, ...) A special node to store the pipeline user-parameters
pipeline_nodes.Switch(pipeline, name, ...[, ...]) Switch node to select a specific Process.

Plug

pipeline.Plug(**kwargs) Overload of the traits in oder to keep the pipeline memory.

Workflow conversion

pipeline_workflow.workflow_from_pipeline(...) Create a soma-workflow workflow from a Capsul Pipeline
pipeline_workflow.workflow_run(...) Create a soma-workflow controller and submit a workflow
pipeline_tools.pipeline_node_colors(...) Node color to display boxes in GUI and graphviz graphs.
pipeline_tools.pipeline_link_color(plug, link) Link color and style for graphical display and graphviz graphs.
pipeline_tools.dot_graph_from_pipeline(pipeline) Build a graphviz/dot-compatible representation of the pipeline.
pipeline_tools.save_dot_graph(dot_graph, ...) Write a graphviz/dot input file, which can be used to generate an image representation of the graph, or to make dot automatically position nodes.
pipeline_tools.save_dot_image(pipeline, filename) Save a dot/graphviz image of the pipeline in a file.
pipeline_tools.nodes_with_existing_outputs(...) Checks nodes in a pipeline which outputs contain existing files on the filesystem.
pipeline_tools.nodes_with_missing_inputs(...) Checks nodes in a pipeline which inputs contain invalid inputs.
pipeline_tools.disable_runtime_steps_with_existing_outputs(...) Disable steps in a pipeline which outputs contain existing files.
pipeline_tools.where_is_plug_value_from(plug) Find where the given (input) plug takes its value from.

capsul.process: Process

Classes

process.Process(**kwargs) A process is an atomic component that contains a processing.
process.NipypeProcess(nipype_instance, ...) Base class used to wrap nipype interfaces.
process.FileCopyProcess([activate_copy, ...]) A specific process that copies all the input files.

Functions

get_process_instance(process_or_id[, ...]) Return a Process instance given an identifier.

capsul.study_config: Study Configuration

Study Configuration

study_config.StudyConfig([study_name, ...]) Class to store the study parameters and processing options.
memory.Memory(cachedir) Memory context to provide caching for processes.

Configuration Modules

somaworkflow_config.SomaWorkflowConfig(...) Configuration module for Soma-Workflow
matlab_config.MatlabConfig(study_config, ...)
spm_config.SPMConfig(study_config, configuration) SPM configuration.
fsl_config.FSLConfig(study_config, configuration)
freesurfer_config.FreeSurferConfig(...) Class to set up freesurfer configuration.
nipype_config.NipypeConfig(study_config, ...) Nipype configuration.
brainvisa_config.BrainVISAConfig(...)
fom_config.FomConfig(study_config, configuration) FOM (File Organization Model) configuration module for StudyConfig
attributes_config.AttributesConfig(...) Attributes-based completion configuration module for StudyConfig
smartcaching_config.SmartCachingConfig(...)

capsul.attributes: Attributes and processes completion

Classes

completion_engine.ProcessCompletionEngine(process) Parameters completion from attributes for a process instance, in the context of a specific data organization.
completion_engine.PathCompletionEngine Implements building of a single path from a set of attributes for a
completion_engine.ProcessCompletionEngineFactory
completion_engine.PathCompletionEngine Implements building of a single path from a set of attributes for a
completion_engine_iteration.ProcessCompletionEngineIteration(process) ProcessCompletionEngine specialization for iterative process.
fom_completion_engine.FomProcessCompletionEngine(process) FOM (File Organization Model) implementation of completion engine.
fom_completion_engine.FomProcessCompletionEngineIteration(process)
fom_completion_engine.FomPathCompletionEngine