skeleton_keys.cmds.depth_profiles_from_aligned_coords.ProfilesFromAlignedCoordsParameters#

class skeleton_keys.cmds.depth_profiles_from_aligned_coords.ProfilesFromAlignedCoordsParameters(*, 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

ProfilesFromAlignedCoordsParameters#
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
coordinate_file	File with specimen IDs on each line	NA	`InputFile`	str
depth_label	label of column with aligned depth values	y	`String`	str
index_label	label of column to split values across rows	None	`String`	str
hist_split_label	label of column to split values across multiple sets of columns	None	`String`	str
layer_depths_file	JSON file with layer depths; used to establish bins for profile histogram	None	`InputFile`	str
bin_size	bin size, in microns	5.0	`Float`	float
below_wm	extent below white matter to include, in microns	200.0	`Float`	float
output_hist_file	output CSV file for depth profiles	aligned_histograms_corrected.csv	`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`