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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

Bases: Node

get_image_metadata(image_name: str = '') → Mapping[str, float | int | str | dict | list]

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

Bases: Node

get_image_metadata(image_name: str = '') → Mapping[str, float | int | str | dict | list]

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

get_image_metadata()

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_image_metadata(image_name: str = '') → Mapping[str, float | int | str | dict | list]

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

get_image_metadata(image_name: str = '') → Mapping[str, float | int | str | dict | list]

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

get_image_metadata(image_name: str = '') → Mapping[str, float | int | str | dict | list]

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

find_summary_file() → str | None

Get this node’s summary file name from the summary list.

If there is no summary file yet, None is returned.

Returns:

Summary file path

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_image_metadata(image_name: str = '') → Mapping[str, float | int | str | dict | list]

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

get_summary_file_name(output_dir: str | None, tag: str | None = None) → str

Get the summary file name

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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

write_summary_file() → None

Write the summary file for this node and add it to the summary list.

write_summary_string_as_text_file(text_str: str, summary_file: str) → None

Write a summary text file with input summary string

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.ProjectMetadataNode(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

get_image_metadata(image_name: str = '')

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

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.TiltSeriesMovieNode(name: str, kwds: List[str] | None = None, do_validation: bool = True, override_format: str = '')

Bases: Node

get_image_metadata(image_name: str = '')

Get metadata about a specific image associated with this node

Simple default implementation to get basic metadata assuming image_name is a path to a file. For richer metadata, or if image_name refers to an item in a STAR file that is not a simple image path, the node-specific class should override this method.

If image_name does not exist or is not an image, this will raise an exception.

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

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.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

class pipeliner.nodes.VisualisationScriptNode(name: str, kwds: List[str] | None = None, toplevel_description: str = 'Scripts that can be opened with Doppio viewers', 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

get_summary_string(output_dir: str | None = None) → str

Generate a summary file for the node

This method should be overridden by every node where a summary needs to be generated

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.add_to_node_summary_list(node_name: str, summary_file: str) → None

Add an entry to the node summary list

Parameters:

• node_name (str) – The name of the node

• summary_file (str) – Path to the summary 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_text(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.get_node_summary_file_from_list(node_name: str) → str | None

Get the summary file for a node from the node summary list.

Returns: the name of the node summary file, or None if there is no entry

for this node name in the summary list.

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

pipeliner.nodes.remove_from_node_summary_list(node_name: str) → None

Remove an entry from the node summary list

Parameters:

node_name (str) – The file to remove