skeleton_keys.cmds.upright_corrected_swc.UprightCorrectedSwcSchema#

class skeleton_keys.cmds.upright_corrected_swc.UprightCorrectedSwcSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet = False, unknown: str | None = None)#

This schema is designed to be a schema_type for an ArgSchemaParser object

UprightCorrectedSwcSchema#
key	description	default	field_type	json_type
input_json	file path of input json file	NA	`InputFile`	str
output_json	file path to output json file	NA	`OutputFile`	str
log_level	set the logging level of the module	ERROR	`LogLevel`	str
specimen_id	Specimen ID	NA	`Integer`	int
swc_path	path to SWC file (optional)	None	`InputFile`	str
output_file	no description	output.swc	`OutputFile`	str
correct_for_shrinkage	Whether to correct for shrinkage	True	`Boolean`	bool
correct_for_slice_angle	Whether to correct for slice angle	True	`Boolean`	bool
surface_and_layers_file	JSON file with surface and layer polygon paths	None	`InputFile`	str
closest_surface_voxel_file	Closest surface voxel reference HDF5 file for slice angle calculation	None	`InputFile`	str
surface_paths_file	Surface paths (streamlines) HDF5 file for slice angle calculation	None	`InputFile`	str

__init__(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet = False, unknown: str | None = None)#

Methods

`__init__`(*[, only, exclude, many, context, ...])
`dump`(obj, *[, many])	Serialize an object to native Python data types according to this Schema's fields.
`dumps`(obj, *args[, many])	Same as `dump()`, except return a JSON-encoded string.
`from_dict`(fields, *[, name])	Generate a Schema class given a dictionary of fields.
`get_attribute`(obj, attr, default)	Defines how to pull values from an object to serialize.
`handle_error`(error, data, , many, *kwargs)	Custom error handler function for the schema.
`load`(data, *[, many, partial, unknown])	Deserialize a data structure to an object defined by this Schema's fields.
`loads`(json_data, *[, many, partial, unknown])	Same as `load()`, except it takes a JSON string as input.
`make_object`(in_data, **kwargs)	marshmallow.pre_load decorated function for applying defaults on deserialation
`on_bind_field`(field_name, field_obj)	Hook to modify a field when it is bound to the Schema.
`validate`(data, *[, many, partial])	Validate data against the schema, returning a dictionary of validation errors.

Attributes

`TYPE_MAPPING`
`dict_class`
`error_messages`	Overrides for default schema-level error messages
`opts`
`set_class`