skeleton_keys.cmds.process_morphology_features.ProcessMorphologyFeaturesParameters#

class skeleton_keys.cmds.process_morphology_features.ProcessMorphologyFeaturesParameters(*, 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

ProcessMorphologyFeaturesParameters#
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_file	File with specimen IDs on each line	NA	`InputFile`	str
swc_paths_file	optional - JSON file with swc file paths keyed on specimen IDs	None	`InputFile`	str
swc_dir	optional - folder to find swc files, assuming specimen_id.swc is filename	None	`InputDir`	str
aligned_depth_profile_file	CSV file with layer-aligned depth profile. If None, depth PCs and EMD features aren’t quantified	None	`InputFile`	str
aligned_soma_file	CSV file with layer-aligned soma depth information. If None, soma depth are not calculated.	None	`InputFile`	str
layer_list	no description	[‘1’, ‘2/3’, ‘4’, ‘5’, ‘6a’, ‘6b’]	`List`	str
analyze_axon	Whether to analyze axon compartments	False	`Boolean`	bool
analyze_basal_dendrite	Whether to analyze basal dendrite compartments	False	`Boolean`	bool
analyze_apical_dendrite	Whether to analyze apical dendrite compartments	False	`Boolean`	bool
analyze_basal_dendrite_depth	Whether to analyze depth profile of basal dendrite compartments	False	`Boolean`	bool
axon_depth_profile_loadings_file	CSV with pre-existing axon depth profile loadings	None	`InputFile`	str
basal_dendrite_depth_profile_loadings_file	CSV with pre-existing basal dendrite depth profile loadings	None	`InputFile`	str
apical_dendrite_depth_profile_loadings_file	CSV with pre-existing apical dendrite depth profile loadings	None	`InputFile`	str
save_axon_depth_profile_loadings_file	Output file to save axon depth profile loadings	None	`OutputFile`	str
save_basal_dendrite_depth_profile_loadings_file	Output file to save basal dendrite depth profile loadings	None	`OutputFile`	str
save_apical_dendrite_depth_profile_loadings_file	Output file to save apical dendrite depth profile loadings	None	`OutputFile`	str
output_file	Long-form CSV of un-normalized features	None	`OutputFile`	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`