Nodes

class pipeliner.nodes.AtomCoordsGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.AtomCoordsNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.DensityMapGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.DensityMapMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.DensityMapNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.EulerAnglesNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.EvaluationMetricNode(name: str, kwds: List[str] | None = None, toplevel_description: str = 'A file containing evaluation metrics', do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.GenNodeFormatConverter(allowed_ext: Dict[Tuple[str, ...], str], check_funct: Dict[str, Callable])

Bases: object

Convert node types for files that have different but equivalent file extensions

allowed_ext

A dict of extensions that are allowed for that nodetype IE: {(“mrc”, “mrcs”, “map”): “mrc”}

Type:: dict

check_funct

A function that checks a file is of the expected type, must return a bool

Type:: staticmethod

gen_nodetype(filename: str, override_format: str = '', validate_file: bool = True) → str

Assign a file to a general node type

Parameters:

filename (str) – File to create the node for
override_format (str) – The node’s format
validate_file (bool) – DO validation on the file type - turn it off to speed up rewriting an entire pipeline

class pipeliner.nodes.Image2DGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.Image2DMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.Image2DNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.Image2DStackNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.Image3DGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.Image3DMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.Image3DNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir)

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.LigandDescriptionNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.LogFileNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.Mask2DNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.Mask3DNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.MicrographCoordsGroupNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.MicrographCoordsNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.MicrographGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.MicrographMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.MicrographMovieGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.MicrographMovieMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.MicrographMovieNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.MicrographNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.MicroscopeDataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.MlModelNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.Node(name: str, toplevel_type: str, kwds: List[str] | None = None, toplevel_description: str = 'A general node type for files without a more specific Node class defined', format_converter: GenNodeFormatConverter | None = None, do_validation: bool = True, override_format: str = '')

Bases: object

Nodes store info about input and output files of jobs that have been run

name

The name of the file the node represents

Type:: str

toplevel_type

The toplevel node type

Type:: str

toplevel_description: (str): A description of the toplevel type

format

The node’s generalised file type IE (‘mrc’ for mrc, ‘mrcs’ or ‘map’)

Type:: str

kwds

Keywords associated with the node

Type:: list[str]

output_from_process

The Process object for process that created the file

Type:: Process

input_for_processes_list

A list of Process objects for processes that use the node as an input

Type:: list

format_converter

An object that defines the expected extensions for the node and how to validate them

Type:: Optional[GenNodeFormatConverter]

type

The full node type

Type:: str

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

generalise_format() → None

Set the node’s format

generalise node format for files that have different but equivalent file extensions EX ‘mrc’ for ‘.map’, or ‘.mrc’ files

defaults to the file extension

get_result_display_object() → ResultsDisplayObject

Get the default results display object for the node.

This method loads the results display object from a saved file on disk if there is one. If not, a new results display object is generated and saved.

Returns:: The default results display object for the node
Return type:: ResultsDisplayObject

load_results_display_file() → ResultsDisplayObject | None

Load the node’s results display object from a file on disk.

This method must be fast because it is used by the GUI to load node results. Therefore, if the display object fails to load properly, no attempt is made to recalculate it and a ResultsDisplayPending object is returned instead.

If there is no results display file yet, None is returned.

Returns:: A ResultsDisplayObject, or None.

not_compatible_with_default_output() → ResultsDisplayObject: Return a ResultsDisplayText object for jobs with no default display object

write_default_result_file() → None: Write the default display file for this node

class pipeliner.nodes.OptimiserDataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.ParamsDataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.ParticleGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

default_results_display(output_dir) → ResultsDisplayObject

Generate a ResultsDisplayObject for the node

This method will be used for every node in Process if there is no ‘create_results_display’ function defined

class pipeliner.nodes.ProcessDataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.RestraintsNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.RigidBodiesNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.SequenceAlignmentNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.SequenceGroupNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.SequenceNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.StructureFactorsNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TiltSeriesGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TiltSeriesMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TiltSeriesMovieGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TiltSeriesMovieMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TiltSeriesMovieNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TiltSeriesNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TomoManifoldDataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TomoOptimisationSetNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TomoTrajectoryDataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TomogramGroupMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TomogramMetadataNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

class pipeliner.nodes.TomogramNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = ''): Bases: Node

pipeliner.nodes.add_to_node_display_file(node_name: str, display_file: str) → None

Add an entry to the node display file

Parameters:

node_name (str) – The name of the node file
display_file (str) – Path to the display file

pipeliner.nodes.check_file_is_cif(file: str) → bool: Validate that a file is a cif or star file

pipeliner.nodes.check_file_is_json(file: str) → bool

pipeliner.nodes.check_file_is_mrc(file: str) → bool: Validate that a file is a mrc file

pipeliner.nodes.check_file_is_text(file: str) → bool

pipeliner.nodes.check_file_is_tif(file: str) → bool

pipeliner.nodes.get_node_results_display_file_name(node_name: str) → str | None

Get the results display file name for a node from the node display file.

Returns: the name of the node results display file, or None if there is no entry: for this node name in the node display file.

pipeliner.nodes.remove_from_node_display_file(node_name: str) → None

Remove an entry from the node display file

Parameters:: node_name (str) – The file to remove