neuron_morphology.feature_extractor.feature_writer

Utilities (mainly the FeatureWriter class) used by the feature extractor executable to format and write outputs.

Module Contents

Classes

FeatureWriter
FeatureFormatter	Format feature results for output

Functions

has_subkey(subkey: str, key: str)	Check whether a string occurs as one of the “.”-separated members of
add_layer_histogram(writer: FeatureWriter, owner: str, key: str, histogram: LayerHistogram) → str	Add a layer histogram to this writer’s heavy data
process_earth_movers_distance(_writer: FeatureWriter, _owner: str, _key: str, value: EarthMoversDistanceResult) → Dict[str, Union[str, float]]	Convert an EarthMoversDistanceResult to a form suitable for json

class neuron_morphology.feature_extractor.feature_writer.FeatureWriter(heavy_path: str, table_path: Optional[str] = None, formatters: Optional[Iterable['FeatureFormatter']] = None, filemode: Optional[str] = 'w')

add_run(self, identifier: str, run: Dict[str, Any])

Add the results of a feature extraction run to this writer

Parameters:

identifier : the unique identifier for this run

run : will be added

process_feature(self, owner: str, key: str, value: Any)

Processes a feature for writing. This may involve:

1. changing its type to something json serializable
2. adding its value to this writer’s heavy output

Parameters:

owner : identifies the reconstruction that owns this feature

key : the name of the feature

value : the feature’s raw value

Returns:

Transformed feature value

write(self)

Write this writer’s output to disk

Returns:

This writer’s outputs as a dictionary

validate_table_extension(self)

If an output table was requested, check that the path has a supported extension.

build_output_table(self)

Convert this writer’s output to a reconstruction X feature table

Returns:

the generated table

write_table(self)

Construct and write a reconstructions X features table from this writer.

register_formatters(self, formatters: Iterable['FeatureFormatter'])

Add formatters to this writer. The order matters! If multiple formatters match a feature, only the first will be applied.

Parameters:

foratters : an ordered collection of formatter to register

neuron_morphology.feature_extractor.feature_writer.FeatureOutputHandler

neuron_morphology.feature_extractor.feature_writer.FeatureOutputCheck

class neuron_morphology.feature_extractor.feature_writer.FeatureFormatter

Bases: typing.NamedTuple

Format feature results for output

name :str

check :FeatureOutputCheck

handler :FeatureOutputHandler

neuron_morphology.feature_extractor.feature_writer.has_subkey(subkey: str, key: str)

Check whether a string occurs as one of the “.”-separated members of another.

neuron_morphology.feature_extractor.feature_writer.add_layer_histogram(writer: FeatureWriter, owner: str, key: str, histogram: LayerHistogram) → str

Add a layer histogram to this writer’s heavy data

Parameters:

owner : identifies the reconstruction that owns this feature

key : the name of the histogram

histogram : the histogram’s data

Returns:

the path at which this writer’s heavy data will be stored

neuron_morphology.feature_extractor.feature_writer.process_earth_movers_distance(_writer: FeatureWriter, _owner: str, _key: str, value: EarthMoversDistanceResult) → Dict[str, Union[str, float]]

Convert an EarthMoversDistanceResult to a form suitable for json serialization

Parameters:

_* : these are unused

value : The result to be transformed

Returns:

a dictionary like:

{

“result”: <float result>, “interpretation” : <name of interpretation enum value>

}

neuron_morphology.feature_extractor.feature_writer.numpy_array_formatter

neuron_morphology.feature_extractor.feature_writer.normalized_depth_histogram_formatter

neuron_morphology.feature_extractor.feature_writer.earth_movers_distance_formatter

neuron_morphology.feature_extractor.feature_writer.DEFAULT_FEATURE_FORMATTERS