:orphan: .. _capsul_ref: ==================================== CAPSUL programming API documentation ==================================== See also the :ref:`capsul_guide` section for more general usage documentation. Classes inheritance diagram =========================== .. inheritance-diagram:: capsul.attributes capsul.attributes.attributes_factory capsul.attributes.attributes_schema capsul.attributes.completion_engine_factory capsul.attributes.completion_engine_iteration capsul.attributes.completion_engine capsul.attributes.fom_completion_engine capsul.engine capsul.engine.database_json capsul.engine.database_populse capsul.engine.database capsul.engine.module capsul.in_context capsul.in_context.fsl capsul.pipeline capsul.pipeline.pipeline capsul.pipeline.pipeline_construction capsul.pipeline.pipeline_nodes capsul.pipeline.pipeline_tools capsul.pipeline.pipeline_workflow capsul.pipeline.process_iteration capsul.pipeline.python_export capsul.pipeline.topological_sort capsul.pipeline.xml capsul.pipeline.custom_nodes capsul.pipeline.custom_nodes.strcat_node capsul.pipeline.custom_nodes.cv_node capsul.pipeline.custom_nodes.loo_node capsul.pipeline.custom_nodes.map_node capsul.pipeline.custom_nodes.reduce_node capsul.plugins capsul.process capsul.process.process capsul.process.nipype_process capsul.process.runprocess capsul.process.xml capsul.qt_apps capsul.qt_apps.utils capsul.qt_apps.utils.application capsul.qt_apps.utils.fill_treectrl capsul.qt_apps.utils.find_pipelines capsul.qt_apps.utils.window capsul.qt_gui capsul.qt_gui.board_widget capsul.qt_gui.widgets capsul.qt_gui.widgets.activation_inspector capsul.qt_gui.widgets.attributed_process_widget capsul.qt_gui.widgets.links_debugger capsul.qt_gui.widgets.pipeline_developer_view capsul.qt_gui.widgets.pipeline_file_warning_widget capsul.qt_gui.widgets.pipeline_user_view capsul.qt_gui.widgets.viewer_widget capsul.sphinxext capsul.sphinxext.layoutdocgen capsul.sphinxext.load_pilots capsul.sphinxext.pipelinedocgen capsul.sphinxext.usecasesdocgen capsul.study_config capsul.study_config.study_config capsul.study_config.config_utils capsul.study_config.memory capsul.study_config.process_instance capsul.study_config.run capsul.study_config.config_modules.attributes_config capsul.study_config.config_modules.brainvisa_config capsul.study_config.config_modules.fom_config capsul.study_config.config_modules.freesurfer_config capsul.study_config.config_modules.fsl_config capsul.study_config.config_modules.matlab_config capsul.study_config.config_modules.nipype_config capsul.study_config.config_modules.smartcaching_config capsul.study_config.config_modules.somaworkflow_config capsul.study_config.config_modules.spm_config capsul.subprocess capsul.subprocess.fsl capsul.subprocess.spm capsul.utils capsul.utils.finder capsul.utils.version_utils :parts: 1 .. capsul.qt_apps.main_window capsul.qt_apps.pipeline_viewer_app Main classes and functions ========================== :mod:`capsul.pipeline`: Pipeline ================================= .. currentmodule:: capsul.pipeline Pipeline Definition ------------------- * :class:`~pipeline.Pipeline` Node Types ---------- .. currentmodule:: capsul.pipeline.pipeline_nodes * :class:`Node` * :class:`ProcessNode` * :class:`PipelineNode` * :class:`Switch` * :mod:`Custom nodes types ` Plug ----- * :class:`Plug` :mod:`capsul.process`: Process =============================== .. currentmodule:: capsul.process.process Classes ------- * :class:`Process` * :class:`NipypeProcess` * :class:`FileCopyProcess` Functions --------- .. currentmodule:: capsul.study_config.process_instance * :func:`get_process_instance` Configuration and execution =========================== :mod:`capsul.engine`: Configuration and execution ------------------------------------------------- This new system will replace :mod:`capsul.study_config` in Capsul v3. .. currentmodule:: capsul.engine Classes: ++++++++ * :class:`CapsulEngine` Functions: ++++++++++ * :func:`capsul_engine` :mod:`capsul.study_config`: Study Configuration ----------------------------------------------- .. currentmodule:: capsul.study_config Study Configuration: ++++++++++++++++++++ * :class:`~study_config.StudyConfig` * :class:`~memory.Memory` Configuration Modules: ++++++++++++++++++++++ .. currentmodule:: capsul.study_config.config_modules * :class:`somaworkflow_config.SomaWorkflowConfig` * :class:`matlab_config.MatlabConfig` * :class:`spm_config.SPMConfig` * :class:`fsl_config.FSLConfig` * :class:`freesurfer_config.FreeSurferConfig` * :class:`nipype_config.NipypeConfig` * :class:`brainvisa_config.BrainVISAConfig` * :class:`fom_config.FomConfig` * :class:`attributes_config.AttributesConfig` * :class:`smartcaching_config.SmartCachingConfig` :mod:`capsul.attributes`: Attributes and processes completion ============================================================= See also the user doc :doc:`../user_guide_tree/advanced_usage`. .. currentmodule:: capsul.attributes Classes ------- * :class:`~completion_engine.ProcessCompletionEngine` * :class:`~completion_engine.PathCompletionEngine` * :class:`~completion_engine.ProcessCompletionEngineFactory` * :class:`~completion_engine.PathCompletionEngine` * :class:`~completion_engine_iteration.ProcessCompletionEngineIteration` * :class:`~fom_completion_engine.FomProcessCompletionEngine` * :class:`~fom_completion_engine.FomProcessCompletionEngineIteration` * :class:`~fom_completion_engine.FomPathCompletionEngine` * :class:`~attributes_schema.AttributesSchema` * :class:`~attributes_schema.ProcessAttributes` * :class:`~attributes_schema.EditableAttributes` Running external software ========================= :mod:`capsul.in_context` ------------------------ The new system which will be used in Capsul v3 is based on :class:`~capsul.engine.CapsulEngine` and is the module: :mod:`~capsul.in_context` :mod:`capsul.subprocess` ------------------------ This module is obsolete and will be replaced by :mod:`~capsul.in_process`. It is still used in Capsul v2 when using :class:`~caspul.study_config.study_config.StudyConfig`. :mod:`capsul.subprocess.fsl` Classes: +++++++++++++++++++++++++++++++++++++ .. currentmodule:: capsul.subprocess.fsl * :class:`Popen` :mod:`capsul.subprocess.fsl` Functions: +++++++++++++++++++++++++++++++++++++++ * :func:`fsl_command_with_environment` * :func:`check_fsl_configuration` * :func:`check_configuration_values` * :func:`auto_configuration` * :func:`call` * :func:`check_call` * :func:`check_output` .. currentmodule:: capsul.subprocess.spm :mod:`capsul.subprocess.spm` Classes: +++++++++++++++++++++++++++++++++++++ * :class:`Popen` :mod:`capsul.subprocess.spm` Functions: +++++++++++++++++++++++++++++++++++++++ * :func:`find_spm` * :func:`check_spm_configuration` * :func:`check_configuration_values` * :func:`auto_configuration` * :func:`spm_command` * :func:`call` * :func:`check_call` * :func:`check_output` Workflow conversion =================== .. currentmodule:: capsul.pipeline.pipeline_workflow * :func:`workflow_from_pipeline` * :func:`workflow_run` .. currentmodule:: capsul.pipeline.pipeline_tools * :func:`dot_graph_from_pipeline` * :func:`save_dot_graph` * :func:`save_dot_image` * :func:`nodes_with_existing_outputs` * :func:`nodes_with_missing_inputs` * :func:`disable_runtime_steps_with_existing_outputs` * :func:`where_is_plug_value_from` GUI === Graphical widgets classes .. _capsul_gui_ref: :mod:`capsul.qt_gui.widgets`: Pipeline Viewers ---------------------------------------------- .. currentmodule:: capsul.qt_gui.widgets * :class:`~pipeline_developer_view.PipelineDeveloperView` * :class:`~pipeline_user_view.PipelineUserView` * :class:`~attributed_process_widget.AttributedProcessWidget` Graphical pipeline debugging tools ---------------------------------- * :class:`~activation_inspector.ActivationInspector` * :class:`~links_debugger.CapsulLinkDebuggerView` Complete modules list ===================== .. toctree:: :maxdepth: 1 api process pipeline engine study_config attributes in_context subprocess utils plugins qt_gui qt_apps sphinxext